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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.expressions-module.html">Package expressions</a> ::
<a href="Bio.expressions.blast-module.html">Package blast</a> ::
Module ncbiblast
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<h1 class="epydoc">Source Code for <a href="Bio.expressions.blast.ncbiblast-module.html">Module Bio.expressions.blast.ncbiblast</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.expressions was deprecated, as it does not work with recent versions of mxTextTools. If you want to continue to use this module, please get in contact with the Biopython developers at biopython-dev@biopython.org to avoid permanent removal of this module from Biopython"</tt><tt class="py-op">,</tt> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">)</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-0', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-1', 'Bio', 'link-1');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Bio.Std=Bio.Std-module.html"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-2', 'Std', 'link-2');">Std</a></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.spaces_line=Bio.expressions.blast.ncbiblast-module.html#spaces_line,Variable Bio.expressions.blast.wublast.spaces_line=Bio.expressions.blast.wublast-module.html#spaces_line"><a title="Bio.expressions.blast.ncbiblast.spaces_line
Bio.expressions.blast.wublast.spaces_line" class="py-name" href="#" onclick="return doclink('link-3', 'spaces_line', 'link-3');">spaces_line</a></tt> <tt class="py-op">=</tt> <tt id="link-4" class="py-name" targets="Function Martel.Opt()=Martel-module.html#Opt"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-4', 'Opt', 'link-4');">Opt</a></tt><tt class="py-op">(</tt><tt id="link-5" class="py-name" targets="Function Martel.Spaces()=Martel-module.html#Spaces"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-5', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-6" class="py-name" targets="Class Martel.Expression.AnyEol=Martel.Expression.AnyEol-class.html"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-6', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt id="link-7" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blast_filter=Bio.expressions.blast.ncbiblast-module.html#blast_filter"><a title="Bio.expressions.blast.ncbiblast.blast_filter" class="py-name" href="#" onclick="return doclink('link-7', 'blast_filter', 'link-7');">blast_filter</a></tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name" targets="Class Martel.Expression.Str=Martel.Expression.Str-class.html,Function Martel.Str()=Martel-module.html#Str"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-8', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"BLASTN"</tt><tt class="py-op">,</tt> <tt class="py-string">"BLASTP"</tt><tt class="py-op">,</tt> <tt class="py-string">"BLASTX"</tt><tt class="py-op">,</tt> <tt class="py-string">"TBLASTX"</tt><tt class="py-op">,</tt> <tt class="py-string">"TBLASTN"</tt><tt class="py-op">)</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt id="link-9" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.ncbi_version=Bio.expressions.blast.ncbiblast-module.html#ncbi_version"><a title="Bio.expressions.blast.ncbiblast.ncbi_version" class="py-name" href="#" onclick="return doclink('link-9', 'ncbi_version', 'link-9');">ncbi_version</a></tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-10', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Function Bio.Std.application_version()=Bio.Std-module.html#application_version"><a title="Bio.Std.application_version" class="py-name" href="#" onclick="return doclink('link-11', 'application_version', 'link-11');">application_version</a></tt><tt class="py-op">(</tt><tt id="link-12" class="py-name" targets="Class Martel.Expression.Group=Martel.Expression.Group-class.html,Function Martel.Group()=Martel-module.html#Group"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-12', 'Group', 'link-12');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"appversion"</tt><tt class="py-op">,</tt> <tt id="link-13" class="py-name" targets="Function Martel.Re()=Martel-module.html#Re"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-13', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"2.\d+\.\d+"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"># BLASTN 2.0.11 [Jan-20-2000]</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-14" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastn_appheader=Bio.expressions.blast.ncbiblast-module.html#blastn_appheader,Variable Bio.expressions.blast.wublast.blastn_appheader=Bio.expressions.blast.wublast-module.html#blastn_appheader"><a title="Bio.expressions.blast.ncbiblast.blastn_appheader
Bio.expressions.blast.wublast.blastn_appheader" class="py-name" href="#" onclick="return doclink('link-14', 'blastn_appheader', 'link-14');">blastn_appheader</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-15" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-15', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Function Bio.Std.application_name()=Bio.Std-module.html#application_name"><a title="Bio.Std.application_name" class="py-name" href="#" onclick="return doclink('link-16', 'application_name', 'link-16');">application_name</a></tt><tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-17', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"BLASTN"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"app"</tt><tt class="py-op">:</tt> <tt class="py-string">"blastn"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt id="link-18" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-18', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt id="link-19" class="py-name"><a title="Bio.expressions.blast.ncbiblast.ncbi_version" class="py-name" href="#" onclick="return doclink('link-19', 'ncbi_version', 'link-9');">ncbi_version</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt id="link-20" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-20', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt id="link-21" class="py-name" targets="Function Martel.ToEol()=Martel-module.html#ToEol"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-21', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-comment"># BLASTP 2.0.11 [Jan-20-2000]</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-22" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastp_appheader=Bio.expressions.blast.ncbiblast-module.html#blastp_appheader,Variable Bio.expressions.blast.wublast.blastp_appheader=Bio.expressions.blast.wublast-module.html#blastp_appheader"><a title="Bio.expressions.blast.ncbiblast.blastp_appheader
Bio.expressions.blast.wublast.blastp_appheader" class="py-name" href="#" onclick="return doclink('link-22', 'blastp_appheader', 'link-22');">blastp_appheader</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-23', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.Std.application_name" class="py-name" href="#" onclick="return doclink('link-24', 'application_name', 'link-16');">application_name</a></tt><tt class="py-op">(</tt><tt id="link-25" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-25', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"BLASTP"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"app"</tt><tt class="py-op">:</tt> <tt class="py-string">"blastp"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt id="link-26" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-26', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt id="link-27" class="py-name"><a title="Bio.expressions.blast.ncbiblast.ncbi_version" class="py-name" href="#" onclick="return doclink('link-27', 'ncbi_version', 'link-9');">ncbi_version</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt id="link-28" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-28', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt id="link-29" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-29', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-comment"># BLASTX 2.0.11 [Jan-20-2000]</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-30" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastx_appheader=Bio.expressions.blast.ncbiblast-module.html#blastx_appheader,Variable Bio.expressions.blast.wublast.blastx_appheader=Bio.expressions.blast.wublast-module.html#blastx_appheader"><a title="Bio.expressions.blast.ncbiblast.blastx_appheader
Bio.expressions.blast.wublast.blastx_appheader" class="py-name" href="#" onclick="return doclink('link-30', 'blastx_appheader', 'link-30');">blastx_appheader</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-31" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-31', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Std.application_name" class="py-name" href="#" onclick="return doclink('link-32', 'application_name', 'link-16');">application_name</a></tt><tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-33', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"BLASTX"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"app"</tt><tt class="py-op">:</tt> <tt class="py-string">"blastx"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt id="link-34" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-34', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt id="link-35" class="py-name"><a title="Bio.expressions.blast.ncbiblast.ncbi_version" class="py-name" href="#" onclick="return doclink('link-35', 'ncbi_version', 'link-9');">ncbi_version</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt id="link-36" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-36', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt id="link-37" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-37', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-comment"># TBLASTN 2.0.11 [Jan-20-2000]</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-38" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.tblastn_appheader=Bio.expressions.blast.ncbiblast-module.html#tblastn_appheader,Variable Bio.expressions.blast.wublast.tblastn_appheader=Bio.expressions.blast.wublast-module.html#tblastn_appheader"><a title="Bio.expressions.blast.ncbiblast.tblastn_appheader
Bio.expressions.blast.wublast.tblastn_appheader" class="py-name" href="#" onclick="return doclink('link-38', 'tblastn_appheader', 'link-38');">tblastn_appheader</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-39', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.Std.application_name" class="py-name" href="#" onclick="return doclink('link-40', 'application_name', 'link-16');">application_name</a></tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-41', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"TBLASTN"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"app"</tt><tt class="py-op">:</tt> <tt class="py-string">"tblastn"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt id="link-42" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-42', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt id="link-43" class="py-name"><a title="Bio.expressions.blast.ncbiblast.ncbi_version" class="py-name" href="#" onclick="return doclink('link-43', 'ncbi_version', 'link-9');">ncbi_version</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt id="link-44" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-44', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt id="link-45" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-45', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-comment"># TBLASTX 2.0.11 [Jan-20-2000]</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-46" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.tblastx_appheader=Bio.expressions.blast.ncbiblast-module.html#tblastx_appheader,Variable Bio.expressions.blast.wublast.tblastx_appheader=Bio.expressions.blast.wublast-module.html#tblastx_appheader"><a title="Bio.expressions.blast.ncbiblast.tblastx_appheader
Bio.expressions.blast.wublast.tblastx_appheader" class="py-name" href="#" onclick="return doclink('link-46', 'tblastx_appheader', 'link-46');">tblastx_appheader</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-47" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-47', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.Std.application_name" class="py-name" href="#" onclick="return doclink('link-48', 'application_name', 'link-16');">application_name</a></tt><tt class="py-op">(</tt><tt id="link-49" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-49', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"TBLASTX"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"app"</tt><tt class="py-op">:</tt> <tt class="py-string">"tblastx"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt id="link-50" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-50', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt id="link-51" class="py-name"><a title="Bio.expressions.blast.ncbiblast.ncbi_version" class="py-name" href="#" onclick="return doclink('link-51', 'ncbi_version', 'link-9');">ncbi_version</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt id="link-52" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-52', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt id="link-53" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-53', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-comment"># This is tricky because the description can include a statement like</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># '(492 letters)' at just the right place to confuse things.</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-54" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.query_letters=Bio.expressions.blast.ncbiblast-module.html#query_letters"><a title="Bio.expressions.blast.ncbiblast.query_letters" class="py-name" href="#" onclick="return doclink('link-54', 'query_letters', 'link-54');">query_letters</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-55" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-55', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt id="link-56" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-56', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"("</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt id="link-57" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-57', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-58" class="py-name" targets="Function Bio.Std.query_size()=Bio.Std-module.html#query_size"><a title="Bio.Std.query_size" class="py-name" href="#" onclick="return doclink('link-58', 'query_size', 'link-58');">query_size</a></tt><tt class="py-op">(</tt><tt id="link-59" class="py-name" targets="Function Martel.Digits()=Martel-module.html#Digits"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-59', 'Digits', 'link-59');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt id="link-60" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-60', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" letters)"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt id="link-61" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-61', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt id="link-62" class="py-name" targets="Function Martel.Assert()=Martel-module.html#Assert,Class Martel.Expression.Assert=Martel.Expression.Assert-class.html"><a title="Martel.Assert
Martel.Expression.Assert" class="py-name" href="#" onclick="return doclink('link-62', 'Assert', 'link-62');">Assert</a></tt><tt class="py-op">(</tt><tt id="link-63" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-63', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt id="link-64" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.query_descr=Bio.expressions.blast.ncbiblast-module.html#query_descr"><a title="Bio.expressions.blast.ncbiblast.query_descr" class="py-name" href="#" onclick="return doclink('link-64', 'query_descr', 'link-64');">query_descr</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-65', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Query="</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt id="link-66" class="py-name"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-66', 'Opt', 'link-4');">Opt</a></tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-67', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt id="link-68" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-68', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-69" class="py-name" targets="Function Bio.Std.query_description()=Bio.Std-module.html#query_description"><a title="Bio.Std.query_description" class="py-name" href="#" onclick="return doclink('link-69', 'query_description', 'link-69');">query_description</a></tt><tt class="py-op">(</tt><tt id="link-70" class="py-name" targets="Function Martel.UntilEol()=Martel-module.html#UntilEol"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-70', 'UntilEol', 'link-70');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt id="link-71" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-71', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt id="link-72" class="py-name" targets="Package Bio.Pathway.Rep=Bio.Pathway.Rep-module.html,Function Martel.Rep()=Martel-module.html#Rep"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-72', 'Rep', 'link-72');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-73" class="py-name" targets="Function Martel.AssertNot()=Martel-module.html#AssertNot"><a title="Martel.AssertNot" class="py-name" href="#" onclick="return doclink('link-73', 'AssertNot', 'link-73');">AssertNot</a></tt><tt class="py-op">(</tt><tt id="link-74" class="py-name"><a title="Bio.expressions.blast.ncbiblast.query_letters" class="py-name" href="#" onclick="return doclink('link-74', 'query_letters', 'link-54');">query_letters</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt id="link-75" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-75', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="Bio.Std.query_description" class="py-name" href="#" onclick="return doclink('link-76', 'query_description', 'link-69');">query_description</a></tt><tt class="py-op">(</tt><tt id="link-77" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-77', 'UntilEol', 'link-70');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt id="link-78" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-78', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt id="link-79" class="py-name"><a title="Bio.expressions.blast.ncbiblast.query_descr" class="py-name" href="#" onclick="return doclink('link-79', 'query_descr', 'link-64');">query_descr</a></tt> <tt class="py-op">=</tt> <tt id="link-80" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-80', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-81" class="py-name" targets="Function Bio.Std.query_description_block()=Bio.Std-module.html#query_description_block"><a title="Bio.Std.query_description_block" class="py-name" href="#" onclick="return doclink('link-81', 'query_description_block', 'link-81');">query_description_block</a></tt><tt class="py-op">(</tt><tt id="link-82" class="py-name"><a title="Bio.expressions.blast.ncbiblast.query_descr" class="py-name" href="#" onclick="return doclink('link-82', 'query_descr', 'link-64');">query_descr</a></tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-comment"># This requires there to be at least one comma</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-83" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast._comma_digits=Bio.expressions.blast.ncbiblast-module.html#_comma_digits"><a title="Bio.expressions.blast.ncbiblast._comma_digits" class="py-name" href="#" onclick="return doclink('link-83', '_comma_digits', 'link-83');">_comma_digits</a></tt> <tt class="py-op">=</tt> <tt id="link-84" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-84', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r"\d(\d\d?)?(,\d\d\d)+"</tt><tt class="py-op">)</tt> </tt>
<a name="Number"></a><div id="Number-def"><a name="L74"></a><tt class="py-lineno"> 74</tt> <a class="py-toggle" href="#" id="Number-toggle" onclick="return toggle('Number');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.expressions.blast.ncbiblast-module.html#Number">Number</a><tt class="py-op">(</tt><tt class="py-param">name</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Number-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Number-expanded"><a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-85" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-85', 'name', 'link-85');">name</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-keyword">not</tt> <tt id="link-86" class="py-name" targets="Variable Martel.Time.attrs=Martel.Time-module.html#attrs"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-86', 'attrs', 'link-86');">attrs</a></tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-87" class="py-name"><a title="Bio.expressions.blast.ncbiblast._comma_digits" class="py-name" href="#" onclick="return doclink('link-87', '_comma_digits', 'link-83');">_comma_digits</a></tt> <tt class="py-op">|</tt> <tt id="link-88" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-88', 'Digits', 'link-59');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-89" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-89', 'Group', 'link-12');">Group</a></tt><tt class="py-op">(</tt><tt id="link-90" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-90', 'name', 'link-85');">name</a></tt><tt class="py-op">,</tt> <tt id="link-91" class="py-name"><a title="Bio.expressions.blast.ncbiblast._comma_digits" class="py-name" href="#" onclick="return doclink('link-91', '_comma_digits', 'link-83');">_comma_digits</a></tt><tt class="py-op">,</tt> <tt id="link-92" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-92', 'attrs', 'link-86');">attrs</a></tt><tt class="py-op">)</tt> <tt class="py-op">|</tt> \ </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt id="link-93" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-93', 'Digits', 'link-59');">Digits</a></tt><tt class="py-op">(</tt><tt id="link-94" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-94', 'name', 'link-85');">name</a></tt><tt class="py-op">,</tt> <tt id="link-95" class="py-name"><a title="Martel.Time.attrs" class="py-name" href="#" onclick="return doclink('link-95', 'attrs', 'link-86');">attrs</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt id="link-96" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.query_database=Bio.expressions.blast.ncbiblast-module.html#query_database,Variable Bio.expressions.blast.wublast.query_database=Bio.expressions.blast.wublast-module.html#query_database"><a title="Bio.expressions.blast.ncbiblast.query_database
Bio.expressions.blast.wublast.query_database" class="py-name" href="#" onclick="return doclink('link-96', 'query_database', 'link-96');">query_database</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-97" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-97', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Database:"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-98" class="py-name"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-98', 'Opt', 'link-4');">Opt</a></tt><tt class="py-op">(</tt><tt id="link-99" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-99', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt id="link-100" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-100', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-101" class="py-name" targets="Function Bio.Std.database_name()=Bio.Std-module.html#database_name"><a title="Bio.Std.database_name" class="py-name" href="#" onclick="return doclink('link-101', 'database_name', 'link-101');">database_name</a></tt><tt class="py-op">(</tt><tt id="link-102" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-102', 'UntilEol', 'link-70');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-103" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-103', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt id="link-104" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-104', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt id="link-105" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-105', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-106" class="py-name" targets="Function Bio.Std.database_num_sequences()=Bio.Std-module.html#database_num_sequences"><a title="Bio.Std.database_num_sequences" class="py-name" href="#" onclick="return doclink('link-106', 'database_num_sequences', 'link-106');">database_num_sequences</a></tt><tt class="py-op">(</tt><tt id="link-107" class="py-name" targets="Function Bio.expressions.blast.ncbiblast.Number()=Bio.expressions.blast.ncbiblast-module.html#Number"><a title="Bio.expressions.blast.ncbiblast.Number" class="py-name" href="#" onclick="return doclink('link-107', 'Number', 'link-107');">Number</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-op">{</tt><tt class="py-string">"bioformat:decode"</tt><tt class="py-op">:</tt> <tt class="py-string">"int.comma"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt id="link-108" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-108', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" sequences;"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-109" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-109', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt id="link-110" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-110', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-111" class="py-name" targets="Function Bio.Std.database_num_letters()=Bio.Std-module.html#database_num_letters"><a title="Bio.Std.database_num_letters" class="py-name" href="#" onclick="return doclink('link-111', 'database_num_letters', 'link-111');">database_num_letters</a></tt><tt class="py-op">(</tt><tt id="link-112" class="py-name"><a title="Bio.expressions.blast.ncbiblast.Number" class="py-name" href="#" onclick="return doclink('link-112', 'Number', 'link-107');">Number</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-op">{</tt><tt class="py-string">"bioformat:decode"</tt><tt class="py-op">:</tt> <tt class="py-string">"int.comma"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt id="link-113" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-113', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-114" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-114', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"total letters"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-115" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-115', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-comment"># Score E</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Sequences producing significant alignments: (bits) Value</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># U51677 Human non-histone chromatin protein HMG1 (HMG1) gene, co... 4129 0.0</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># L38477 Mus musculus (clone Clebp-1) high mobility group 1 prote... 353 7e-95</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt id="link-116" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.to_table=Bio.expressions.blast.ncbiblast-module.html#to_table,Variable Bio.expressions.blast.wublast.to_table=Bio.expressions.blast.wublast-module.html#to_table"><a title="Bio.expressions.blast.ncbiblast.to_table
Bio.expressions.blast.wublast.to_table" class="py-name" href="#" onclick="return doclink('link-116', 'to_table', 'link-116');">to_table</a></tt> <tt class="py-op">=</tt> <tt id="link-117" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-117', 'Group', 'link-12');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"to_table"</tt><tt class="py-op">,</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-118" class="py-name" targets="Function Martel.SkipLinesUntil()=Martel-module.html#SkipLinesUntil"><a title="Martel.SkipLinesUntil" class="py-name" href="#" onclick="return doclink('link-118', 'SkipLinesUntil', 'link-118');">SkipLinesUntil</a></tt><tt class="py-op">(</tt><tt id="link-119" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-119', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Sequences producing significant"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt id="link-120" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-120', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt id="link-121" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-121', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt id="link-122" class="py-name" targets="Variable Bio.CDD.cdd_format.table_entry=Bio.CDD.cdd_format-module.html#table_entry,Variable Bio.expressions.blast.ncbiblast.table_entry=Bio.expressions.blast.ncbiblast-module.html#table_entry,Variable Bio.expressions.blast.wublast.table_entry=Bio.expressions.blast.wublast-module.html#table_entry"><a title="Bio.CDD.cdd_format.table_entry
Bio.expressions.blast.ncbiblast.table_entry
Bio.expressions.blast.wublast.table_entry" class="py-name" href="#" onclick="return doclink('link-122', 'table_entry', 'link-122');">table_entry</a></tt> <tt class="py-op">=</tt> <tt id="link-123" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-123', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-124" class="py-name" targets="Function Bio.Std.search_table_entry()=Bio.Std-module.html#search_table_entry"><a title="Bio.Std.search_table_entry" class="py-name" href="#" onclick="return doclink('link-124', 'search_table_entry', 'link-124');">search_table_entry</a></tt><tt class="py-op">(</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt id="link-125" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-125', 'Group', 'link-12');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"table_entry"</tt><tt class="py-op">,</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-126" class="py-name"><a title="Martel.AssertNot" class="py-name" href="#" onclick="return doclink('link-126', 'AssertNot', 'link-73');">AssertNot</a></tt><tt class="py-op">(</tt><tt id="link-127" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-127', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt id="link-128" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-128', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-129" class="py-name" targets="Function Bio.Std.search_table_description()=Bio.Std-module.html#search_table_description"><a title="Bio.Std.search_table_description" class="py-name" href="#" onclick="return doclink('link-129', 'search_table_description', 'link-129');">search_table_description</a></tt><tt class="py-op">(</tt><tt id="link-130" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-130', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r".{66}"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-131" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-131', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt id="link-132" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-132', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-133" class="py-name" targets="Function Bio.Std.search_table_value()=Bio.Std-module.html#search_table_value"><a title="Bio.Std.search_table_value" class="py-name" href="#" onclick="return doclink('link-133', 'search_table_value', 'link-133');">search_table_value</a></tt><tt class="py-op">(</tt><tt id="link-134" class="py-name" targets="Class Bio.Decode.Float=Bio.Decode.Float-class.html,Function Martel.Float()=Martel-module.html#Float"><a title="Bio.Decode.Float
Martel.Float" class="py-name" href="#" onclick="return doclink('link-134', 'Float', 'link-134');">Float</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"name"</tt><tt class="py-op">:</tt> <tt class="py-string">"score"</tt><tt class="py-op">,</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-string">"bioformat:decode"</tt><tt class="py-op">:</tt> <tt class="py-string">"float"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt id="link-135" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-135', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt id="link-136" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-136', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="Bio.Std.search_table_value" class="py-name" href="#" onclick="return doclink('link-137', 'search_table_value', 'link-133');">search_table_value</a></tt><tt class="py-op">(</tt><tt id="link-138" class="py-name"><a title="Bio.Decode.Float
Martel.Float" class="py-name" href="#" onclick="return doclink('link-138', 'Float', 'link-134');">Float</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"name"</tt><tt class="py-op">:</tt> <tt class="py-string">"evalue"</tt><tt class="py-op">,</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-string">"bioformat:decode"</tt><tt class="py-op">:</tt> <tt class="py-string">"float"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt id="link-139" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-139', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt id="link-140" class="py-name" targets="Variable Bio.CDD.cdd_format.table=Bio.CDD.cdd_format-module.html#table,Variable Bio.expressions.blast.ncbiblast.table=Bio.expressions.blast.ncbiblast-module.html#table"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-140', 'table', 'link-140');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-141" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-141', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-142" class="py-name" targets="Function Bio.Std.search_table()=Bio.Std-module.html#search_table"><a title="Bio.Std.search_table" class="py-name" href="#" onclick="return doclink('link-142', 'search_table', 'link-142');">search_table</a></tt><tt class="py-op">(</tt><tt id="link-143" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-143', 'Rep', 'link-72');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-144" class="py-name"><a title="Bio.CDD.cdd_format.table_entry
Bio.expressions.blast.ncbiblast.table_entry
Bio.expressions.blast.wublast.table_entry" class="py-name" href="#" onclick="return doclink('link-144', 'table_entry', 'link-122');">table_entry</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt id="link-145" class="py-name" targets="Variable Bio.Wise.dnal.Statistics.header=Bio.Wise.dnal.Statistics-class.html#header,Variable Bio.expressions.blast.ncbiblast.header=Bio.expressions.blast.ncbiblast-module.html#header,Variable Bio.expressions.blast.wublast.header=Bio.expressions.blast.wublast-module.html#header,Variable Bio.expressions.blocks.header=Bio.expressions.blocks-module.html#header,Variable Bio.expressions.genbank.header=Bio.expressions.genbank-module.html#header,Variable Bio.expressions.hmmpfam.header=Bio.expressions.hmmpfam-module.html#header"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-145', 'header', 'link-145');">header</a></tt> <tt class="py-op">=</tt> <tt id="link-146" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-146', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-147" class="py-name" targets="Function Bio.Std.search_header()=Bio.Std-module.html#search_header"><a title="Bio.Std.search_header" class="py-name" href="#" onclick="return doclink('link-147', 'search_header', 'link-147');">search_header</a></tt><tt class="py-op">(</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt id="link-148" class="py-name"><a title="Martel.SkipLinesUntil" class="py-name" href="#" onclick="return doclink('link-148', 'SkipLinesUntil', 'link-118');">SkipLinesUntil</a></tt><tt class="py-op">(</tt><tt id="link-149" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-149', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Query="</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt id="link-150" class="py-name"><a title="Bio.expressions.blast.ncbiblast.query_descr" class="py-name" href="#" onclick="return doclink('link-150', 'query_descr', 'link-64');">query_descr</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt id="link-151" class="py-name"><a title="Bio.expressions.blast.ncbiblast.query_letters" class="py-name" href="#" onclick="return doclink('link-151', 'query_letters', 'link-54');">query_letters</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt id="link-152" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-152', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt id="link-153" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-153', 'Group', 'link-12');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"to_database"</tt><tt class="py-op">,</tt> <tt id="link-154" class="py-name" targets="Class Martel.Expression.NullOp=Martel.Expression.NullOp-class.html"><a title="Martel.Expression.NullOp" class="py-name" href="#" onclick="return doclink('link-154', 'NullOp', 'link-154');">NullOp</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-comment"># Needed for wu-blastx</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt id="link-155" class="py-name"><a title="Bio.expressions.blast.ncbiblast.query_database
Bio.expressions.blast.wublast.query_database" class="py-name" href="#" onclick="return doclink('link-155', 'query_database', 'link-96');">query_database</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt id="link-156" class="py-name"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-156', 'Opt', 'link-4');">Opt</a></tt><tt class="py-op">(</tt><tt id="link-157" class="py-name"><a title="Bio.expressions.blast.ncbiblast.to_table
Bio.expressions.blast.wublast.to_table" class="py-name" href="#" onclick="return doclink('link-157', 'to_table', 'link-116');">to_table</a></tt> <tt class="py-op">+</tt> <tt id="link-158" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-158', 'table', 'link-140');">table</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt id="link-159" class="py-name"><a title="Martel.SkipLinesUntil" class="py-name" href="#" onclick="return doclink('link-159', 'SkipLinesUntil', 'link-118');">SkipLinesUntil</a></tt><tt class="py-op">(</tt><tt id="link-160" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-160', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">">"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-comment"># >U51677 Human non-histone chromatin protein HMG1 (HMG1) gene, complete</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># cds.</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Length = 2575</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Score = 4129 bits (2083), Expect = 0.0</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Identities = 2167/2209 (98%)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Strand = Plus / Plus</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-comment"># This is tricky since it's (theoretical) possible the description</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># could have a "Length =" at exactly the right spot to confuse things.</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># So stop before getting to the line with a 'Length =' where the</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># line afterwards is blank.</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-161" class="py-name" targets="Function Bio.Std.hit_length()=Bio.Std-module.html#hit_length,Variable Bio.expressions.blast.ncbiblast.hit_length=Bio.expressions.blast.ncbiblast-module.html#hit_length,Variable Bio.expressions.blast.wublast.hit_length=Bio.expressions.blast.wublast-module.html#hit_length"><a title="Bio.Std.hit_length
Bio.expressions.blast.ncbiblast.hit_length
Bio.expressions.blast.wublast.hit_length" class="py-name" href="#" onclick="return doclink('link-161', 'hit_length', 'link-161');">hit_length</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-162" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-162', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-163" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-163', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Length = "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt id="link-164" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-164', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-165" class="py-name"><a title="Bio.Std.hit_length
Bio.expressions.blast.ncbiblast.hit_length
Bio.expressions.blast.wublast.hit_length" class="py-name" href="#" onclick="return doclink('link-165', 'hit_length', 'link-161');">hit_length</a></tt><tt class="py-op">(</tt><tt id="link-166" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-166', 'Digits', 'link-59');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-167" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-167', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt id="link-168" class="py-name"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-168', 'Opt', 'link-4');">Opt</a></tt><tt class="py-op">(</tt><tt id="link-169" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-169', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-170" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-170', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt id="link-171" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.hit_descr=Bio.expressions.blast.ncbiblast-module.html#hit_descr,Variable Bio.expressions.blast.wublast.hit_descr=Bio.expressions.blast.wublast-module.html#hit_descr"><a title="Bio.expressions.blast.ncbiblast.hit_descr
Bio.expressions.blast.wublast.hit_descr" class="py-name" href="#" onclick="return doclink('link-171', 'hit_descr', 'link-171');">hit_descr</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-172" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-172', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">">"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-173" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-173', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-174" class="py-name" targets="Function Bio.Std.hit_description()=Bio.Std-module.html#hit_description"><a title="Bio.Std.hit_description" class="py-name" href="#" onclick="return doclink('link-174', 'hit_description', 'link-174');">hit_description</a></tt><tt class="py-op">(</tt><tt id="link-175" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-175', 'UntilEol', 'link-70');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-176" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-176', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt id="link-177" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-177', 'Rep', 'link-72');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-178" class="py-name"><a title="Martel.AssertNot" class="py-name" href="#" onclick="return doclink('link-178', 'AssertNot', 'link-73');">AssertNot</a></tt><tt class="py-op">(</tt><tt id="link-179" class="py-name"><a title="Bio.Std.hit_length
Bio.expressions.blast.ncbiblast.hit_length
Bio.expressions.blast.wublast.hit_length" class="py-name" href="#" onclick="return doclink('link-179', 'hit_length', 'link-161');">hit_length</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt id="link-180" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-180', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-181" class="py-name"><a title="Bio.Std.hit_description" class="py-name" href="#" onclick="return doclink('link-181', 'hit_description', 'link-174');">hit_description</a></tt><tt class="py-op">(</tt><tt id="link-182" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-182', 'UntilEol', 'link-70');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-183" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-183', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt id="link-184" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.num_bits=Bio.expressions.blast.ncbiblast-module.html#num_bits"><a title="Bio.expressions.blast.ncbiblast.num_bits" class="py-name" href="#" onclick="return doclink('link-184', 'num_bits', 'link-184');">num_bits</a></tt> <tt class="py-op">=</tt> <tt id="link-185" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-185', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-186" class="py-name" targets="Function Bio.Std.hsp_value()=Bio.Std-module.html#hsp_value"><a title="Bio.Std.hsp_value" class="py-name" href="#" onclick="return doclink('link-186', 'hsp_value', 'link-186');">hsp_value</a></tt><tt class="py-op">(</tt><tt id="link-187" class="py-name"><a title="Bio.Decode.Float
Martel.Float" class="py-name" href="#" onclick="return doclink('link-187', 'Float', 'link-134');">Float</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"name"</tt><tt class="py-op">:</tt> <tt class="py-string">"bits"</tt><tt class="py-op">,</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-string">"bioformat:decode"</tt><tt class="py-op">:</tt> <tt class="py-string">"float"</tt><tt class="py-op">,</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt id="link-188" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.expect=Bio.expressions.blast.ncbiblast-module.html#expect"><a title="Bio.expressions.blast.ncbiblast.expect" class="py-name" href="#" onclick="return doclink('link-188', 'expect', 'link-188');">expect</a></tt> <tt class="py-op">=</tt> <tt id="link-189" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-189', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-190" class="py-name"><a title="Bio.Std.hsp_value" class="py-name" href="#" onclick="return doclink('link-190', 'hsp_value', 'link-186');">hsp_value</a></tt><tt class="py-op">(</tt><tt id="link-191" class="py-name"><a title="Bio.Decode.Float
Martel.Float" class="py-name" href="#" onclick="return doclink('link-191', 'Float', 'link-134');">Float</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"name"</tt><tt class="py-op">:</tt> <tt class="py-string">"expect"</tt><tt class="py-op">,</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-string">"bioformat:decode"</tt><tt class="py-op">:</tt> <tt class="py-string">"float"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt id="link-192" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.num_identical=Bio.expressions.blast.ncbiblast-module.html#num_identical"><a title="Bio.expressions.blast.ncbiblast.num_identical" class="py-name" href="#" onclick="return doclink('link-192', 'num_identical', 'link-192');">num_identical</a></tt> <tt class="py-op">=</tt> <tt id="link-193" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-193', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-194" class="py-name"><a title="Bio.Std.hsp_value" class="py-name" href="#" onclick="return doclink('link-194', 'hsp_value', 'link-186');">hsp_value</a></tt><tt class="py-op">(</tt><tt id="link-195" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-195', 'Digits', 'link-59');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"name"</tt><tt class="py-op">:</tt> <tt class="py-string">"identical"</tt><tt class="py-op">,</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-string">"bioformat:decode"</tt><tt class="py-op">:</tt> <tt class="py-string">"int"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt id="link-196" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.hsp_length=Bio.expressions.blast.ncbiblast-module.html#hsp_length"><a title="Bio.expressions.blast.ncbiblast.hsp_length" class="py-name" href="#" onclick="return doclink('link-196', 'hsp_length', 'link-196');">hsp_length</a></tt> <tt class="py-op">=</tt> <tt id="link-197" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-197', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-198" class="py-name"><a title="Bio.Std.hsp_value" class="py-name" href="#" onclick="return doclink('link-198', 'hsp_value', 'link-186');">hsp_value</a></tt><tt class="py-op">(</tt><tt id="link-199" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-199', 'Digits', 'link-59');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"name"</tt><tt class="py-op">:</tt> <tt class="py-string">"length"</tt><tt class="py-op">,</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-string">"bioformat:decode"</tt><tt class="py-op">:</tt> <tt class="py-string">"int"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt id="link-200" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.num_positives=Bio.expressions.blast.ncbiblast-module.html#num_positives"><a title="Bio.expressions.blast.ncbiblast.num_positives" class="py-name" href="#" onclick="return doclink('link-200', 'num_positives', 'link-200');">num_positives</a></tt> <tt class="py-op">=</tt> <tt id="link-201" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-201', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-202" class="py-name"><a title="Bio.Std.hsp_value" class="py-name" href="#" onclick="return doclink('link-202', 'hsp_value', 'link-186');">hsp_value</a></tt><tt class="py-op">(</tt><tt id="link-203" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-203', 'Digits', 'link-59');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"name"</tt><tt class="py-op">:</tt> <tt class="py-string">"positives"</tt><tt class="py-op">,</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-string">"bioformat:decode"</tt><tt class="py-op">:</tt> <tt class="py-string">"int"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-comment"># What's after the bits?</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-204" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.score()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#score,Variable Bio.expressions.blast.ncbiblast.score=Bio.expressions.blast.ncbiblast-module.html#score"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-204', 'score', 'link-204');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-205" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-205', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r" *Score = *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-206" class="py-name"><a title="Bio.expressions.blast.ncbiblast.num_bits" class="py-name" href="#" onclick="return doclink('link-206', 'num_bits', 'link-184');">num_bits</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt id="link-207" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-207', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r" bits \((?P<XXX1>\d+)\), Expect = *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt id="link-208" class="py-name"><a title="Bio.expressions.blast.ncbiblast.expect" class="py-name" href="#" onclick="return doclink('link-208', 'expect', 'link-188');">expect</a></tt> <tt class="py-op">+</tt> <tt id="link-209" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-209', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-comment"># XXX What's the expect_num mean?</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-210" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.tblastn_score=Bio.expressions.blast.ncbiblast-module.html#tblastn_score,Variable Bio.expressions.blast.wublast.tblastn_score=Bio.expressions.blast.wublast-module.html#tblastn_score"><a title="Bio.expressions.blast.ncbiblast.tblastn_score
Bio.expressions.blast.wublast.tblastn_score" class="py-name" href="#" onclick="return doclink('link-210', 'tblastn_score', 'link-210');">tblastn_score</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-211" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-211', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r" *Score = *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-212" class="py-name"><a title="Bio.expressions.blast.ncbiblast.num_bits" class="py-name" href="#" onclick="return doclink('link-212', 'num_bits', 'link-184');">num_bits</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt id="link-213" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-213', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r" bits \((?P<XXX1>\d+)\), "</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-string">r"Expect(\((?P<expect_num>\d+)\))? = *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt id="link-214" class="py-name"><a title="Bio.expressions.blast.ncbiblast.expect" class="py-name" href="#" onclick="return doclink('link-214', 'expect', 'link-188');">expect</a></tt> <tt class="py-op">+</tt> <tt id="link-215" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-215', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt id="link-216" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastn_identical=Bio.expressions.blast.ncbiblast-module.html#blastn_identical"><a title="Bio.expressions.blast.ncbiblast.blastn_identical" class="py-name" href="#" onclick="return doclink('link-216', 'blastn_identical', 'link-216');">blastn_identical</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-217" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-217', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r" *Identities = *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt id="link-218" class="py-name"><a title="Bio.expressions.blast.ncbiblast.num_identical" class="py-name" href="#" onclick="return doclink('link-218', 'num_identical', 'link-192');">num_identical</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt id="link-219" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-219', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"/"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt id="link-220" class="py-name"><a title="Bio.expressions.blast.ncbiblast.hsp_length" class="py-name" href="#" onclick="return doclink('link-220', 'hsp_length', 'link-196');">hsp_length</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt id="link-221" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-221', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-comment"># Identities = 154/168 (91%), Positives = 154/168 (91%)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-222" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastp_identical=Bio.expressions.blast.ncbiblast-module.html#blastp_identical"><a title="Bio.expressions.blast.ncbiblast.blastp_identical" class="py-name" href="#" onclick="return doclink('link-222', 'blastp_identical', 'link-222');">blastp_identical</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-223" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-223', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r" *Identities = *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt id="link-224" class="py-name"><a title="Bio.expressions.blast.ncbiblast.num_identical" class="py-name" href="#" onclick="return doclink('link-224', 'num_identical', 'link-192');">num_identical</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt id="link-225" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-225', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"/"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt id="link-226" class="py-name"><a title="Bio.expressions.blast.ncbiblast.hsp_length" class="py-name" href="#" onclick="return doclink('link-226', 'hsp_length', 'link-196');">hsp_length</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt id="link-227" class="py-name" targets="Function Martel.ToSep()=Martel-module.html#ToSep"><a title="Martel.ToSep" class="py-name" href="#" onclick="return doclink('link-227', 'ToSep', 'link-227');">ToSep</a></tt><tt class="py-op">(</tt><tt class="py-name">sep</tt> <tt class="py-op">=</tt> <tt class="py-string">","</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt id="link-228" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-228', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">" Positives = *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt id="link-229" class="py-name"><a title="Bio.expressions.blast.ncbiblast.num_positives" class="py-name" href="#" onclick="return doclink('link-229', 'num_positives', 'link-200');">num_positives</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt id="link-230" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-230', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-comment"># Frame = +1</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># can be +1, +2, +3, -1, -2, -3</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-231" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.frame()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#frame,Variable Bio.expressions.blast.ncbiblast.frame=Bio.expressions.blast.ncbiblast-module.html#frame"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.frame
Bio.expressions.blast.ncbiblast.frame" class="py-name" href="#" onclick="return doclink('link-231', 'frame', 'link-231');">frame</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-232" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-232', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" Frame = "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-233" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-233', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-234" class="py-name" targets="Function Bio.Std.hsp_frame()=Bio.Std-module.html#hsp_frame"><a title="Bio.Std.hsp_frame" class="py-name" href="#" onclick="return doclink('link-234', 'hsp_frame', 'link-234');">hsp_frame</a></tt><tt class="py-op">(</tt><tt id="link-235" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-235', 'UntilEol', 'link-70');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"which"</tt><tt class="py-op">:</tt> <tt class="py-string">"query"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt id="link-236" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-236', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt id="link-237" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.tblastx_frame=Bio.expressions.blast.ncbiblast-module.html#tblastx_frame"><a title="Bio.expressions.blast.ncbiblast.tblastx_frame" class="py-name" href="#" onclick="return doclink('link-237', 'tblastx_frame', 'link-237');">tblastx_frame</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-238" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-238', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" Frame = "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt id="link-239" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-239', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-240" class="py-name"><a title="Bio.Std.hsp_frame" class="py-name" href="#" onclick="return doclink('link-240', 'hsp_frame', 'link-234');">hsp_frame</a></tt><tt class="py-op">(</tt><tt id="link-241" class="py-name" targets="Function Martel.UntilSep()=Martel-module.html#UntilSep"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-241', 'UntilSep', 'link-241');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-name">sep</tt> <tt class="py-op">=</tt> <tt class="py-string">" "</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"which"</tt><tt class="py-op">:</tt> <tt class="py-string">"query"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt id="link-242" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-242', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" / "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt id="link-243" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-243', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-244" class="py-name"><a title="Bio.Std.hsp_frame" class="py-name" href="#" onclick="return doclink('link-244', 'hsp_frame', 'link-234');">hsp_frame</a></tt><tt class="py-op">(</tt><tt id="link-245" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-245', 'UntilEol', 'link-70');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"which"</tt><tt class="py-op">:</tt> <tt class="py-string">"subject"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt id="link-246" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-246', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-comment"># Strand = Plus / Plus</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-247" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.strand()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#strand,Variable Bio.expressions.blast.ncbiblast.strand=Bio.expressions.blast.ncbiblast-module.html#strand"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-247', 'strand', 'link-247');">strand</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-248" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-248', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r" *Strand = "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-249" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-249', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-250" class="py-name" targets="Function Bio.Std.hsp_strand()=Bio.Std-module.html#hsp_strand"><a title="Bio.Std.hsp_strand" class="py-name" href="#" onclick="return doclink('link-250', 'hsp_strand', 'link-250');">hsp_strand</a></tt><tt class="py-op">(</tt><tt id="link-251" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-251', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Plus"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"strand"</tt><tt class="py-op">:</tt> <tt class="py-string">"+1"</tt><tt class="py-op">,</tt> <tt class="py-string">"which"</tt><tt class="py-op">:</tt> <tt class="py-string">"query"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">|</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt id="link-252" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-252', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-253" class="py-name"><a title="Bio.Std.hsp_strand" class="py-name" href="#" onclick="return doclink('link-253', 'hsp_strand', 'link-250');">hsp_strand</a></tt><tt class="py-op">(</tt><tt id="link-254" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-254', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Minus"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"strand"</tt><tt class="py-op">:</tt> <tt class="py-string">"-1"</tt><tt class="py-op">,</tt> <tt class="py-string">"which"</tt><tt class="py-op">:</tt> <tt class="py-string">"query"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt id="link-255" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-255', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" / "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-256" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-256', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-257" class="py-name"><a title="Bio.Std.hsp_strand" class="py-name" href="#" onclick="return doclink('link-257', 'hsp_strand', 'link-250');">hsp_strand</a></tt><tt class="py-op">(</tt><tt id="link-258" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-258', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Plus"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"strand"</tt><tt class="py-op">:</tt> <tt class="py-string">"+1"</tt><tt class="py-op">,</tt> <tt class="py-string">"which"</tt><tt class="py-op">:</tt> <tt class="py-string">"subject"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> <tt class="py-op">|</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt id="link-259" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-259', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-260" class="py-name"><a title="Bio.Std.hsp_strand" class="py-name" href="#" onclick="return doclink('link-260', 'hsp_strand', 'link-250');">hsp_strand</a></tt><tt class="py-op">(</tt><tt id="link-261" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-261', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Minus"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"strand"</tt><tt class="py-op">:</tt> <tt class="py-string">"-1"</tt><tt class="py-op">,</tt> <tt class="py-string">"which"</tt><tt class="py-op">:</tt> <tt class="py-string">"subject"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">+</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt id="link-262" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-262', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt id="link-263" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.query_line=Bio.expressions.blast.ncbiblast-module.html#query_line"><a title="Bio.expressions.blast.ncbiblast.query_line" class="py-name" href="#" onclick="return doclink('link-263', 'query_line', 'link-263');">query_line</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt id="link-264" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-264', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-265" class="py-name" targets="Function Bio.Std.hsp_seqalign_query_leader()=Bio.Std-module.html#hsp_seqalign_query_leader"><a title="Bio.Std.hsp_seqalign_query_leader" class="py-name" href="#" onclick="return doclink('link-265', 'hsp_seqalign_query_leader', 'link-265');">hsp_seqalign_query_leader</a></tt><tt class="py-op">(</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt id="link-266" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-266', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-267" class="py-name" targets="Function Bio.Std.hsp_seqalign_query_name()=Bio.Std-module.html#hsp_seqalign_query_name"><a title="Bio.Std.hsp_seqalign_query_name" class="py-name" href="#" onclick="return doclink('link-267', 'hsp_seqalign_query_name', 'link-267');">hsp_seqalign_query_name</a></tt><tt class="py-op">(</tt><tt id="link-268" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-268', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Query"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt id="link-269" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-269', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">": *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt id="link-270" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-270', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-271" class="py-name" targets="Function Bio.Std.hsp_seqalign_query_start()=Bio.Std-module.html#hsp_seqalign_query_start"><a title="Bio.Std.hsp_seqalign_query_start" class="py-name" href="#" onclick="return doclink('link-271', 'hsp_seqalign_query_start', 'link-271');">hsp_seqalign_query_start</a></tt><tt class="py-op">(</tt><tt id="link-272" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-272', 'Digits', 'link-59');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt id="link-273" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-273', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">" *"</tt><tt class="py-op">)</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt id="link-274" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-274', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-275" class="py-name" targets="Function Bio.Std.hsp_seqalign_query_seq()=Bio.Std-module.html#hsp_seqalign_query_seq"><a title="Bio.Std.hsp_seqalign_query_seq" class="py-name" href="#" onclick="return doclink('link-275', 'hsp_seqalign_query_seq', 'link-275');">hsp_seqalign_query_seq</a></tt><tt class="py-op">(</tt><tt id="link-276" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-276', 'UntilSep', 'link-241');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-name">sep</tt> <tt class="py-op">=</tt> <tt class="py-string">" "</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt id="link-277" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-277', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">" *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt id="link-278" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-278', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-279" class="py-name" targets="Function Bio.Std.hsp_seqalign_query_end()=Bio.Std-module.html#hsp_seqalign_query_end"><a title="Bio.Std.hsp_seqalign_query_end" class="py-name" href="#" onclick="return doclink('link-279', 'hsp_seqalign_query_end', 'link-279');">hsp_seqalign_query_end</a></tt><tt class="py-op">(</tt><tt id="link-280" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-280', 'Digits', 'link-59');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt id="link-281" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-281', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt id="link-282" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.homology_line=Bio.expressions.blast.ncbiblast-module.html#homology_line"><a title="Bio.expressions.blast.ncbiblast.homology_line" class="py-name" href="#" onclick="return doclink('link-282', 'homology_line', 'link-282');">homology_line</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt id="link-283" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-283', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-284" class="py-name" targets="Function Bio.Std.hsp_seqalign_homology_seq()=Bio.Std-module.html#hsp_seqalign_homology_seq"><a title="Bio.Std.hsp_seqalign_homology_seq" class="py-name" href="#" onclick="return doclink('link-284', 'hsp_seqalign_homology_seq', 'link-284');">hsp_seqalign_homology_seq</a></tt><tt class="py-op">(</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt id="link-285" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-285', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-comment"># The blanks are for safety; to</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt id="link-286" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-286', 'UntilEol', 'link-70');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment"># ensure we don't blindly read a line</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt id="link-287" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-287', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt id="link-288" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.subject_line=Bio.expressions.blast.ncbiblast-module.html#subject_line"><a title="Bio.expressions.blast.ncbiblast.subject_line" class="py-name" href="#" onclick="return doclink('link-288', 'subject_line', 'link-288');">subject_line</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt id="link-289" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-289', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-290" class="py-name" targets="Function Bio.Std.hsp_seqalign_subject_name()=Bio.Std-module.html#hsp_seqalign_subject_name"><a title="Bio.Std.hsp_seqalign_subject_name" class="py-name" href="#" onclick="return doclink('link-290', 'hsp_seqalign_subject_name', 'link-290');">hsp_seqalign_subject_name</a></tt><tt class="py-op">(</tt><tt id="link-291" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-291', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Sbjct"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt id="link-292" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-292', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">": *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt id="link-293" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-293', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-294" class="py-name" targets="Function Bio.Std.hsp_seqalign_subject_start()=Bio.Std-module.html#hsp_seqalign_subject_start"><a title="Bio.Std.hsp_seqalign_subject_start" class="py-name" href="#" onclick="return doclink('link-294', 'hsp_seqalign_subject_start', 'link-294');">hsp_seqalign_subject_start</a></tt><tt class="py-op">(</tt><tt id="link-295" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-295', 'Digits', 'link-59');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt id="link-296" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-296', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">" *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt id="link-297" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-297', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-298" class="py-name" targets="Function Bio.Std.hsp_seqalign_subject_seq()=Bio.Std-module.html#hsp_seqalign_subject_seq"><a title="Bio.Std.hsp_seqalign_subject_seq" class="py-name" href="#" onclick="return doclink('link-298', 'hsp_seqalign_subject_seq', 'link-298');">hsp_seqalign_subject_seq</a></tt><tt class="py-op">(</tt><tt id="link-299" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-299', 'UntilSep', 'link-241');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-name">sep</tt> <tt class="py-op">=</tt> <tt class="py-string">" "</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt id="link-300" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-300', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">" *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt id="link-301" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-301', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-302" class="py-name" targets="Function Bio.Std.hsp_seqalign_subject_end()=Bio.Std-module.html#hsp_seqalign_subject_end"><a title="Bio.Std.hsp_seqalign_subject_end" class="py-name" href="#" onclick="return doclink('link-302', 'hsp_seqalign_subject_end', 'link-302');">hsp_seqalign_subject_end</a></tt><tt class="py-op">(</tt><tt id="link-303" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-303', 'Digits', 'link-59');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt id="link-304" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-304', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt id="link-305" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastn_hsp_header=Bio.expressions.blast.ncbiblast-module.html#blastn_hsp_header,Variable Bio.expressions.blast.wublast.blastn_hsp_header=Bio.expressions.blast.wublast-module.html#blastn_hsp_header"><a title="Bio.expressions.blast.ncbiblast.blastn_hsp_header
Bio.expressions.blast.wublast.blastn_hsp_header" class="py-name" href="#" onclick="return doclink('link-305', 'blastn_hsp_header', 'link-305');">blastn_hsp_header</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-306" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-306', 'score', 'link-204');">score</a></tt> <tt class="py-op">+</tt> <tt id="link-307" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastn_identical" class="py-name" href="#" onclick="return doclink('link-307', 'blastn_identical', 'link-216');">blastn_identical</a></tt> <tt class="py-op">+</tt> <tt id="link-308" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-308', 'strand', 'link-247');">strand</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt id="link-309" class="py-name"><a title="Bio.expressions.blast.ncbiblast.spaces_line
Bio.expressions.blast.wublast.spaces_line" class="py-name" href="#" onclick="return doclink('link-309', 'spaces_line', 'link-3');">spaces_line</a></tt> <tt class="py-op">+</tt> <tt id="link-310" class="py-name"><a title="Bio.expressions.blast.ncbiblast.spaces_line
Bio.expressions.blast.wublast.spaces_line" class="py-name" href="#" onclick="return doclink('link-310', 'spaces_line', 'link-3');">spaces_line</a></tt><tt class="py-op">)</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt id="link-311" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastp_hsp_header=Bio.expressions.blast.ncbiblast-module.html#blastp_hsp_header,Variable Bio.expressions.blast.wublast.blastp_hsp_header=Bio.expressions.blast.wublast-module.html#blastp_hsp_header"><a title="Bio.expressions.blast.ncbiblast.blastp_hsp_header
Bio.expressions.blast.wublast.blastp_hsp_header" class="py-name" href="#" onclick="return doclink('link-311', 'blastp_hsp_header', 'link-311');">blastp_hsp_header</a></tt> <tt class="py-op">=</tt> <tt id="link-312" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-312', 'score', 'link-204');">score</a></tt> <tt class="py-op">+</tt> <tt id="link-313" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastp_identical" class="py-name" href="#" onclick="return doclink('link-313', 'blastp_identical', 'link-222');">blastp_identical</a></tt> <tt class="py-op">+</tt> <tt id="link-314" class="py-name"><a title="Bio.expressions.blast.ncbiblast.spaces_line
Bio.expressions.blast.wublast.spaces_line" class="py-name" href="#" onclick="return doclink('link-314', 'spaces_line', 'link-3');">spaces_line</a></tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt id="link-315" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastx_hsp_header=Bio.expressions.blast.ncbiblast-module.html#blastx_hsp_header,Variable Bio.expressions.blast.wublast.blastx_hsp_header=Bio.expressions.blast.wublast-module.html#blastx_hsp_header"><a title="Bio.expressions.blast.ncbiblast.blastx_hsp_header
Bio.expressions.blast.wublast.blastx_hsp_header" class="py-name" href="#" onclick="return doclink('link-315', 'blastx_hsp_header', 'link-315');">blastx_hsp_header</a></tt> <tt class="py-op">=</tt> <tt id="link-316" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-316', 'score', 'link-204');">score</a></tt> <tt class="py-op">+</tt> <tt id="link-317" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastp_identical" class="py-name" href="#" onclick="return doclink('link-317', 'blastp_identical', 'link-222');">blastp_identical</a></tt> <tt class="py-op">+</tt> <tt id="link-318" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.frame
Bio.expressions.blast.ncbiblast.frame" class="py-name" href="#" onclick="return doclink('link-318', 'frame', 'link-231');">frame</a></tt> <tt class="py-op">+</tt> <tt id="link-319" class="py-name"><a title="Bio.expressions.blast.ncbiblast.spaces_line
Bio.expressions.blast.wublast.spaces_line" class="py-name" href="#" onclick="return doclink('link-319', 'spaces_line', 'link-3');">spaces_line</a></tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"><tt id="link-320" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.tblastn_hsp_header=Bio.expressions.blast.ncbiblast-module.html#tblastn_hsp_header,Variable Bio.expressions.blast.wublast.tblastn_hsp_header=Bio.expressions.blast.wublast-module.html#tblastn_hsp_header"><a title="Bio.expressions.blast.ncbiblast.tblastn_hsp_header
Bio.expressions.blast.wublast.tblastn_hsp_header" class="py-name" href="#" onclick="return doclink('link-320', 'tblastn_hsp_header', 'link-320');">tblastn_hsp_header</a></tt> <tt class="py-op">=</tt> <tt id="link-321" class="py-name"><a title="Bio.expressions.blast.ncbiblast.tblastn_score
Bio.expressions.blast.wublast.tblastn_score" class="py-name" href="#" onclick="return doclink('link-321', 'tblastn_score', 'link-210');">tblastn_score</a></tt> <tt class="py-op">+</tt> <tt id="link-322" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastp_identical" class="py-name" href="#" onclick="return doclink('link-322', 'blastp_identical', 'link-222');">blastp_identical</a></tt> <tt class="py-op">+</tt> <tt id="link-323" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.frame
Bio.expressions.blast.ncbiblast.frame" class="py-name" href="#" onclick="return doclink('link-323', 'frame', 'link-231');">frame</a></tt> <tt class="py-op">+</tt> <tt id="link-324" class="py-name"><a title="Bio.expressions.blast.ncbiblast.spaces_line
Bio.expressions.blast.wublast.spaces_line" class="py-name" href="#" onclick="return doclink('link-324', 'spaces_line', 'link-3');">spaces_line</a></tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt id="link-325" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.tblastx_hsp_header=Bio.expressions.blast.ncbiblast-module.html#tblastx_hsp_header"><a title="Bio.expressions.blast.ncbiblast.tblastx_hsp_header" class="py-name" href="#" onclick="return doclink('link-325', 'tblastx_hsp_header', 'link-325');">tblastx_hsp_header</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-326" class="py-name"><a title="Bio.expressions.blast.ncbiblast.tblastn_score
Bio.expressions.blast.wublast.tblastn_score" class="py-name" href="#" onclick="return doclink('link-326', 'tblastn_score', 'link-210');">tblastn_score</a></tt> <tt class="py-op">+</tt> <tt id="link-327" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastp_identical" class="py-name" href="#" onclick="return doclink('link-327', 'blastp_identical', 'link-222');">blastp_identical</a></tt> <tt class="py-op">+</tt> <tt id="link-328" class="py-name"><a title="Bio.expressions.blast.ncbiblast.tblastx_frame" class="py-name" href="#" onclick="return doclink('link-328', 'tblastx_frame', 'link-237');">tblastx_frame</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt id="link-329" class="py-name"><a title="Bio.expressions.blast.ncbiblast.spaces_line
Bio.expressions.blast.wublast.spaces_line" class="py-name" href="#" onclick="return doclink('link-329', 'spaces_line', 'link-3');">spaces_line</a></tt> <tt class="py-op">+</tt> <tt id="link-330" class="py-name"><a title="Bio.expressions.blast.ncbiblast.spaces_line
Bio.expressions.blast.wublast.spaces_line" class="py-name" href="#" onclick="return doclink('link-330', 'spaces_line', 'link-3');">spaces_line</a></tt><tt class="py-op">)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"><tt id="link-331" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.alignment=Bio.expressions.blast.ncbiblast-module.html#alignment"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-331', 'alignment', 'link-331');">alignment</a></tt> <tt class="py-op">=</tt> <tt id="link-332" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-332', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-333" class="py-name" targets="Function Bio.Std.hsp_seqalign()=Bio.Std-module.html#hsp_seqalign"><a title="Bio.Std.hsp_seqalign" class="py-name" href="#" onclick="return doclink('link-333', 'hsp_seqalign', 'link-333');">hsp_seqalign</a></tt><tt class="py-op">(</tt><tt id="link-334" class="py-name"><a title="Bio.expressions.blast.ncbiblast.query_line" class="py-name" href="#" onclick="return doclink('link-334', 'query_line', 'link-263');">query_line</a></tt> <tt class="py-op">+</tt> <tt id="link-335" class="py-name"><a title="Bio.expressions.blast.ncbiblast.homology_line" class="py-name" href="#" onclick="return doclink('link-335', 'homology_line', 'link-282');">homology_line</a></tt> <tt class="py-op">+</tt> <tt id="link-336" class="py-name"><a title="Bio.expressions.blast.ncbiblast.subject_line" class="py-name" href="#" onclick="return doclink('link-336', 'subject_line', 'link-288');">subject_line</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt id="link-337" class="py-name" targets="Function Martel.Rep1()=Martel-module.html#Rep1"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-337', 'Rep1', 'link-337');">Rep1</a></tt><tt class="py-op">(</tt><tt id="link-338" class="py-name"><a title="Bio.expressions.blast.ncbiblast.spaces_line
Bio.expressions.blast.wublast.spaces_line" class="py-name" href="#" onclick="return doclink('link-338', 'spaces_line', 'link-3');">spaces_line</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt id="link-339" class="py-name" targets="Function Bio.Std.hsp()=Bio.Std-module.html#hsp,Variable Bio.expressions.blast.ncbiblast.hsp=Bio.expressions.blast.ncbiblast-module.html#hsp"><a title="Bio.Std.hsp
Bio.expressions.blast.ncbiblast.hsp" class="py-name" href="#" onclick="return doclink('link-339', 'hsp', 'link-339');">hsp</a></tt> <tt class="py-op">=</tt> <tt id="link-340" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-340', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-341" class="py-name"><a title="Bio.Std.hsp
Bio.expressions.blast.ncbiblast.hsp" class="py-name" href="#" onclick="return doclink('link-341', 'hsp', 'link-339');">hsp</a></tt><tt class="py-op">(</tt><tt id="link-342" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-342', 'Group', 'link-12');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"hsp_header"</tt><tt class="py-op">,</tt> <tt id="link-343" class="py-name"><a title="Martel.Expression.NullOp" class="py-name" href="#" onclick="return doclink('link-343', 'NullOp', 'link-154');">NullOp</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt id="link-344" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-344', 'Rep', 'link-72');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-345" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-345', 'alignment', 'link-331');">alignment</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt id="link-346" class="py-name" targets="Function Bio.Std.hit()=Bio.Std-module.html#hit,Variable Bio.expressions.blast.ncbiblast.hit=Bio.expressions.blast.ncbiblast-module.html#hit"><a title="Bio.Std.hit
Bio.expressions.blast.ncbiblast.hit" class="py-name" href="#" onclick="return doclink('link-346', 'hit', 'link-346');">hit</a></tt> <tt class="py-op">=</tt> <tt id="link-347" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-347', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-348" class="py-name"><a title="Bio.Std.hit
Bio.expressions.blast.ncbiblast.hit" class="py-name" href="#" onclick="return doclink('link-348', 'hit', 'link-346');">hit</a></tt><tt class="py-op">(</tt><tt id="link-349" class="py-name"><a title="Bio.expressions.blast.ncbiblast.hit_descr
Bio.expressions.blast.wublast.hit_descr" class="py-name" href="#" onclick="return doclink('link-349', 'hit_descr', 'link-171');">hit_descr</a></tt> <tt class="py-op">+</tt> <tt id="link-350" class="py-name"><a title="Bio.Std.hit_length
Bio.expressions.blast.ncbiblast.hit_length
Bio.expressions.blast.wublast.hit_length" class="py-name" href="#" onclick="return doclink('link-350', 'hit_length', 'link-161');">hit_length</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt id="link-351" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-351', 'Rep', 'link-72');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-352" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-352', 'Group', 'link-12');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"hsp"</tt><tt class="py-op">,</tt> <tt id="link-353" class="py-name"><a title="Bio.Std.hsp
Bio.expressions.blast.ncbiblast.hsp" class="py-name" href="#" onclick="return doclink('link-353', 'hsp', 'link-339');">hsp</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-comment"># Already know the database</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"><tt class="py-comment"># parse the name: value lines</tt> </tt>
<a name="_nv"></a><div id="_nv-def"><a name="L275"></a><tt class="py-lineno">275</tt> <a class="py-toggle" href="#" id="_nv-toggle" onclick="return toggle('_nv');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.expressions.blast.ncbiblast-module.html#_nv">_nv</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">expr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_nv-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_nv-expanded"><a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-354" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-354', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt id="link-355" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-355', 's', 'link-355');">s</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">expr</tt> <tt class="py-op">+</tt> <tt id="link-356" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-356', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="float_stat"></a><div id="float_stat-def"><a name="L277"></a><tt class="py-lineno">277</tt> <a class="py-toggle" href="#" id="float_stat-toggle" onclick="return toggle('float_stat');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.expressions.blast.ncbiblast-module.html#float_stat">float_stat</a><tt class="py-op">(</tt><tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="float_stat-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="float_stat-expanded"><a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-357" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-357', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-358" class="py-name" targets="Function Bio.Std.search_statistic()=Bio.Std-module.html#search_statistic"><a title="Bio.Std.search_statistic" class="py-name" href="#" onclick="return doclink('link-358', 'search_statistic', 'link-358');">search_statistic</a></tt><tt class="py-op">(</tt><tt id="link-359" class="py-name"><a title="Bio.Decode.Float
Martel.Float" class="py-name" href="#" onclick="return doclink('link-359', 'Float', 'link-134');">Float</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"name"</tt><tt class="py-op">:</tt> <tt id="link-360" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-360', 'name', 'link-85');">name</a></tt><tt class="py-op">,</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-string">"bioformat:decode"</tt><tt class="py-op">:</tt> <tt class="py-string">"float"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
</div><a name="_num_stat"></a><div id="_num_stat-def"><a name="L280"></a><tt class="py-lineno">280</tt> <a class="py-toggle" href="#" id="_num_stat-toggle" onclick="return toggle('_num_stat');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.expressions.blast.ncbiblast-module.html#_num_stat">_num_stat</a><tt class="py-op">(</tt><tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">signed</tt><tt class="py-op">,</tt> <tt class="py-param">comma</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_num_stat-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_num_stat-expanded"><a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt id="link-361" class="py-name" targets="Variable Bio.EUtils.setup.d=Bio.EUtils.setup-module.html#d"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-361', 'd', 'link-361');">d</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"name"</tt><tt class="py-op">:</tt> <tt id="link-362" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-362', 'name', 'link-85');">name</a></tt><tt class="py-op">,</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-string">"bioformat:decode"</tt><tt class="py-op">:</tt> <tt class="py-string">"int"</tt><tt class="py-op">}</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">signed</tt><tt class="py-op">:</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt id="link-363" class="py-name" targets="Variable Bio.Affy.CelFile.exp=Bio.Affy.CelFile-module.html#exp,Variable Bio.LogisticRegression.exp=Bio.LogisticRegression-module.html#exp,Variable Bio.MarkovModel.exp=Bio.MarkovModel-module.html#exp,Variable Bio.MaxEntropy.exp=Bio.MaxEntropy-module.html#exp,Variable Bio.NaiveBayes.exp=Bio.NaiveBayes-module.html#exp,Variable Bio.Statistics.lowess.exp=Bio.Statistics.lowess-module.html#exp,Variable Bio.distance.exp=Bio.distance-module.html#exp,Variable Bio.kNN.exp=Bio.kNN-module.html#exp"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-363', 'exp', 'link-363');">exp</a></tt> <tt class="py-op">=</tt> <tt id="link-364" class="py-name" targets="Class Bio.Decode.Integer=Bio.Decode.Integer-class.html,Class Bio.GenBank.LocationParser.Integer=Bio.GenBank.LocationParser.Integer-class.html,Function Martel.Integer()=Martel-module.html#Integer"><a title="Bio.Decode.Integer
Bio.GenBank.LocationParser.Integer
Martel.Integer" class="py-name" href="#" onclick="return doclink('link-364', 'Integer', 'link-364');">Integer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">comma</tt><tt class="py-op">:</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt id="link-365" class="py-name"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-365', 'exp', 'link-363');">exp</a></tt> <tt class="py-op">=</tt> <tt id="link-366" class="py-name"><a title="Bio.expressions.blast.ncbiblast.Number" class="py-name" href="#" onclick="return doclink('link-366', 'Number', 'link-107');">Number</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt id="link-367" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-367', 'd', 'link-361');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">"bioformat:decode"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">"int.comma"</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt id="link-368" class="py-name"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-368', 'exp', 'link-363');">exp</a></tt> <tt class="py-op">=</tt> <tt id="link-369" class="py-name"><a title="Martel.Digits" class="py-name" href="#" onclick="return doclink('link-369', 'Digits', 'link-59');">Digits</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-370" class="py-name"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-370', 'exp', 'link-363');">exp</a></tt><tt class="py-op">,</tt> <tt id="link-371" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-371', 'd', 'link-361');">d</a></tt> </tt>
</div><a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> </tt>
<a name="int_stat"></a><div id="int_stat-def"><a name="L292"></a><tt class="py-lineno">292</tt> <a class="py-toggle" href="#" id="int_stat-toggle" onclick="return toggle('int_stat');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.expressions.blast.ncbiblast-module.html#int_stat">int_stat</a><tt class="py-op">(</tt><tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">signed</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">comma</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="int_stat-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="int_stat-expanded"><a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt id="link-372" class="py-name"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-372', 'exp', 'link-363');">exp</a></tt><tt class="py-op">,</tt> <tt id="link-373" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-373', 'd', 'link-361');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-374" class="py-name" targets="Function Bio.expressions.blast.ncbiblast._num_stat()=Bio.expressions.blast.ncbiblast-module.html#_num_stat"><a title="Bio.expressions.blast.ncbiblast._num_stat" class="py-name" href="#" onclick="return doclink('link-374', '_num_stat', 'link-374');">_num_stat</a></tt><tt class="py-op">(</tt><tt id="link-375" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-375', 'name', 'link-85');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">signed</tt><tt class="py-op">,</tt> <tt class="py-name">comma</tt><tt class="py-op">)</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-376" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-376', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-377" class="py-name"><a title="Bio.Std.search_statistic" class="py-name" href="#" onclick="return doclink('link-377', 'search_statistic', 'link-358');">search_statistic</a></tt><tt class="py-op">(</tt><tt id="link-378" class="py-name"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-378', 'exp', 'link-363');">exp</a></tt><tt class="py-op">,</tt> <tt id="link-379" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-379', 'd', 'link-361');">d</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> </tt>
<a name="int_param"></a><div id="int_param-def"><a name="L296"></a><tt class="py-lineno">296</tt> <a class="py-toggle" href="#" id="int_param-toggle" onclick="return toggle('int_param');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.expressions.blast.ncbiblast-module.html#int_param">int_param</a><tt class="py-op">(</tt><tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">signed</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">comma</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="int_param-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="int_param-expanded"><a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt id="link-380" class="py-name"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-380', 'exp', 'link-363');">exp</a></tt><tt class="py-op">,</tt> <tt id="link-381" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-381', 'd', 'link-361');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-382" class="py-name"><a title="Bio.expressions.blast.ncbiblast._num_stat" class="py-name" href="#" onclick="return doclink('link-382', '_num_stat', 'link-374');">_num_stat</a></tt><tt class="py-op">(</tt><tt id="link-383" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-383', 'name', 'link-85');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">signed</tt><tt class="py-op">,</tt> <tt class="py-name">comma</tt><tt class="py-op">)</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-384" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-384', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-385" class="py-name" targets="Function Bio.Std.search_parameter()=Bio.Std-module.html#search_parameter"><a title="Bio.Std.search_parameter" class="py-name" href="#" onclick="return doclink('link-385', 'search_parameter', 'link-385');">search_parameter</a></tt><tt class="py-op">(</tt><tt id="link-386" class="py-name"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-386', 'exp', 'link-363');">exp</a></tt><tt class="py-op">,</tt> <tt id="link-387" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-387', 'd', 'link-361');">d</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> </tt>
<a name="float_param"></a><div id="float_param-def"><a name="L300"></a><tt class="py-lineno">300</tt> <a class="py-toggle" href="#" id="float_param-toggle" onclick="return toggle('float_param');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.expressions.blast.ncbiblast-module.html#float_param">float_param</a><tt class="py-op">(</tt><tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="float_param-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="float_param-expanded"><a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-388" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-388', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-389" class="py-name"><a title="Bio.Std.search_parameter" class="py-name" href="#" onclick="return doclink('link-389', 'search_parameter', 'link-385');">search_parameter</a></tt><tt class="py-op">(</tt><tt id="link-390" class="py-name"><a title="Bio.Decode.Float
Martel.Float" class="py-name" href="#" onclick="return doclink('link-390', 'Float', 'link-134');">Float</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"name"</tt><tt class="py-op">:</tt> <tt id="link-391" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-391', 'name', 'link-85');">name</a></tt><tt class="py-op">,</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-string">"bioformat:decode"</tt><tt class="py-op">:</tt> <tt class="py-string">"float"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
</div><a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt id="link-392" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.db_stats=Bio.expressions.blast.ncbiblast-module.html#db_stats"><a title="Bio.expressions.blast.ncbiblast.db_stats" class="py-name" href="#" onclick="return doclink('link-392', 'db_stats', 'link-392');">db_stats</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-393" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-393', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" Database:"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-394" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-394', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt id="link-395" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-395', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" Posted date:"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-396" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-396', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt id="link-397" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-397', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" Number of letters"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-398" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-398', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt id="link-399" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-399', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" Number of sequences"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-400" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-400', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt id="link-401" class="py-name"><a title="Bio.expressions.blast.ncbiblast.spaces_line
Bio.expressions.blast.wublast.spaces_line" class="py-name" href="#" onclick="return doclink('link-401', 'spaces_line', 'link-3');">spaces_line</a></tt><tt class="py-op">)</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"><tt id="link-402" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.ungapped_lambda_stats=Bio.expressions.blast.ncbiblast-module.html#ungapped_lambda_stats"><a title="Bio.expressions.blast.ncbiblast.ungapped_lambda_stats" class="py-name" href="#" onclick="return doclink('link-402', 'ungapped_lambda_stats', 'link-402');">ungapped_lambda_stats</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt id="link-403" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-403', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Lambda K H"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-404" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-404', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-op">(</tt> <tt id="link-405" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-405', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-406" class="py-name" targets="Function Bio.expressions.blast.ncbiblast.float_stat()=Bio.expressions.blast.ncbiblast-module.html#float_stat"><a title="Bio.expressions.blast.ncbiblast.float_stat" class="py-name" href="#" onclick="return doclink('link-406', 'float_stat', 'link-406');">float_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"lambda"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt id="link-407" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-407', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-408" class="py-name"><a title="Bio.expressions.blast.ncbiblast.float_stat" class="py-name" href="#" onclick="return doclink('link-408', 'float_stat', 'link-406');">float_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"k"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt id="link-409" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-409', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-410" class="py-name"><a title="Bio.expressions.blast.ncbiblast.float_stat" class="py-name" href="#" onclick="return doclink('link-410', 'float_stat', 'link-406');">float_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"h"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt id="link-411" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-411', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"><tt id="link-412" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.gapped_lambda_stats=Bio.expressions.blast.ncbiblast-module.html#gapped_lambda_stats"><a title="Bio.expressions.blast.ncbiblast.gapped_lambda_stats" class="py-name" href="#" onclick="return doclink('link-412', 'gapped_lambda_stats', 'link-412');">gapped_lambda_stats</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt id="link-413" class="py-name"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-413', 'Opt', 'link-4');">Opt</a></tt><tt class="py-op">(</tt><tt id="link-414" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-414', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Gapped"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-415" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-415', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt id="link-416" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-416', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Lambda K H"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-417" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-417', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-op">(</tt> <tt id="link-418" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-418', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-419" class="py-name"><a title="Bio.expressions.blast.ncbiblast.float_stat" class="py-name" href="#" onclick="return doclink('link-419', 'float_stat', 'link-406');">float_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"gapped_lambda"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt id="link-420" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-420', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-421" class="py-name"><a title="Bio.expressions.blast.ncbiblast.float_stat" class="py-name" href="#" onclick="return doclink('link-421', 'float_stat', 'link-406');">float_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"gapped_k"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt id="link-422" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-422', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-423" class="py-name"><a title="Bio.expressions.blast.ncbiblast.float_stat" class="py-name" href="#" onclick="return doclink('link-423', 'float_stat', 'link-406');">float_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"gapped_h"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt id="link-424" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-424', 'ToEol', 'link-21');">ToEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"><tt id="link-425" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.lambda_stats=Bio.expressions.blast.ncbiblast-module.html#lambda_stats"><a title="Bio.expressions.blast.ncbiblast.lambda_stats" class="py-name" href="#" onclick="return doclink('link-425', 'lambda_stats', 'link-425');">lambda_stats</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-426" class="py-name"><a title="Bio.expressions.blast.ncbiblast.ungapped_lambda_stats" class="py-name" href="#" onclick="return doclink('link-426', 'ungapped_lambda_stats', 'link-402');">ungapped_lambda_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt id="link-427" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-427', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt id="link-428" class="py-name"><a title="Bio.expressions.blast.ncbiblast.gapped_lambda_stats" class="py-name" href="#" onclick="return doclink('link-428', 'gapped_lambda_stats', 'link-412');">gapped_lambda_stats</a></tt><tt class="py-op">)</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"><tt id="link-429" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.matrix_stats=Bio.expressions.blast.ncbiblast-module.html#matrix_stats"><a title="Bio.expressions.blast.ncbiblast.matrix_stats" class="py-name" href="#" onclick="return doclink('link-429', 'matrix_stats', 'link-429');">matrix_stats</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt id="link-430" class="py-name"><a title="Martel.SkipLinesUntil" class="py-name" href="#" onclick="return doclink('link-430', 'SkipLinesUntil', 'link-118');">SkipLinesUntil</a></tt><tt class="py-op">(</tt><tt id="link-431" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-431', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"Matrix:"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-comment"># Matrix: blastn matrix:1 -3</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt id="link-432" class="py-name" targets="Function Bio.expressions.blast.ncbiblast._nv()=Bio.expressions.blast.ncbiblast-module.html#_nv"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-432', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"Matrix: "</tt><tt class="py-op">,</tt> <tt id="link-433" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-433', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-434" class="py-name"><a title="Bio.Std.search_statistic" class="py-name" href="#" onclick="return doclink('link-434', 'search_statistic', 'link-358');">search_statistic</a></tt><tt class="py-op">(</tt><tt id="link-435" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-435', 'UntilEol', 'link-70');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-string">"name"</tt><tt class="py-op">:</tt> <tt class="py-string">"matrix"</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"><tt id="link-436" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.gap_penalties_stats=Bio.expressions.blast.ncbiblast-module.html#gap_penalties_stats"><a title="Bio.expressions.blast.ncbiblast.gap_penalties_stats" class="py-name" href="#" onclick="return doclink('link-436', 'gap_penalties_stats', 'link-436');">gap_penalties_stats</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-comment"># Gap Penalties: Existence: 5, Extension: 2</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt id="link-437" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-437', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"Gap Penalties: Existence: "</tt><tt class="py-op">,</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt id="link-438" class="py-name" targets="Function Bio.expressions.blast.ncbiblast.int_param()=Bio.expressions.blast.ncbiblast-module.html#int_param"><a title="Bio.expressions.blast.ncbiblast.int_param" class="py-name" href="#" onclick="return doclink('link-438', 'int_param', 'link-438');">int_param</a></tt><tt class="py-op">(</tt><tt class="py-string">"existence_gap_penalty"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt id="link-439" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-439', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">", Extension: "</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt id="link-440" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_param" class="py-name" href="#" onclick="return doclink('link-440', 'int_param', 'link-438');">int_param</a></tt><tt class="py-op">(</tt><tt class="py-string">"extension_gap_penalty"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"><tt id="link-441" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.generic_info1=Bio.expressions.blast.ncbiblast-module.html#generic_info1"><a title="Bio.expressions.blast.ncbiblast.generic_info1" class="py-name" href="#" onclick="return doclink('link-441', 'generic_info1', 'link-441');">generic_info1</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-comment"># Number of Hits to DB: 1123218</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-comment"># !! I've seen negative numbers here !!</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-comment"># Number of Hits to DB: -331804600</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt id="link-442" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-442', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"Number of Hits to DB: "</tt><tt class="py-op">,</tt> <tt id="link-443" class="py-name" targets="Function Bio.expressions.blast.ncbiblast.int_stat()=Bio.expressions.blast.ncbiblast-module.html#int_stat"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-443', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"num_hits_to_db"</tt><tt class="py-op">,</tt> <tt class="py-name">signed</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-comment"># Number of Sequences: 442729</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt id="link-444" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-444', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"Number of Sequences: "</tt><tt class="py-op">,</tt> <tt id="link-445" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-445', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"num_sequences"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-comment"># Number of extensions: 1123218</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt id="link-446" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-446', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"Number of extensions: "</tt><tt class="py-op">,</tt> <tt id="link-447" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-447', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"num_extensions"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-comment"># Number of successful extensions: 86816</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt id="link-448" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-448', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"Number of successful extensions: "</tt><tt class="py-op">,</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt id="link-449" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-449', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"num_successful_extensions"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-comment"># Number of sequences better than 10.0: 106</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt id="link-450" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-450', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"Number of sequences better than 10.0: "</tt><tt class="py-op">,</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt id="link-451" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-451', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"num_sequences_better_than_10"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"><tt id="link-452" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.generic_info2=Bio.expressions.blast.ncbiblast-module.html#generic_info2"><a title="Bio.expressions.blast.ncbiblast.generic_info2" class="py-name" href="#" onclick="return doclink('link-452', 'generic_info2', 'link-452');">generic_info2</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-comment"># length of query: 2575</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt id="link-453" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-453', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"length of query: "</tt><tt class="py-op">,</tt> <tt id="link-454" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-454', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"query_length"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-comment"># length of database: 675,252,082</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt id="link-455" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-455', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"length of database: "</tt><tt class="py-op">,</tt> <tt id="link-456" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-456', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"database_length"</tt><tt class="py-op">,</tt> <tt class="py-name">comma</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-comment"># effective HSP length: 21</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt id="link-457" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-457', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"effective HSP length: "</tt><tt class="py-op">,</tt> <tt id="link-458" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-458', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"effective_hsp_length"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">+</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-comment"># effective length of query: 2554</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt id="link-459" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-459', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"effective length of query: "</tt><tt class="py-op">,</tt> <tt id="link-460" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-460', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"effective_query_length"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-comment"># effective length of database: 665,954,773</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt id="link-461" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-461', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"effective length of database: "</tt><tt class="py-op">,</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt id="link-462" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-462', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"effective_database_length"</tt><tt class="py-op">,</tt> <tt class="py-name">comma</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-comment"># effective search space: 1700848490242</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt id="link-463" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-463', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"effective search space: "</tt><tt class="py-op">,</tt> <tt id="link-464" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-464', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"effective_search_space"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-comment"># effective search space used: 1700848490242</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt id="link-465" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-465', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"effective search space used: "</tt><tt class="py-op">,</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt id="link-466" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-466', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"effective_search_space_used"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"><tt id="link-467" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.hsp_info=Bio.expressions.blast.ncbiblast-module.html#hsp_info"><a title="Bio.expressions.blast.ncbiblast.hsp_info" class="py-name" href="#" onclick="return doclink('link-467', 'hsp_info', 'link-467');">hsp_info</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-comment"># Number of HSP's better than 10.0 without gapping: 136</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt id="link-468" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-468', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"Number of HSP's better than 10.0 without gapping: "</tt><tt class="py-op">,</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt id="link-469" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-469', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"num_hsps_better_than_10_without_gapping"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt class="py-comment"># Number of HSP's successfully gapped in prelim test: 14</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt id="link-470" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-470', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"Number of HSP's successfully gapped in prelim test: "</tt><tt class="py-op">,</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt id="link-471" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-471', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"num_hsps_successfully_gapped_in_prelim_test"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-comment"># Number of HSP's that attempted gapping in prelim test: 880</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt id="link-472" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-472', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"Number of HSP's that attempted gapping in prelim test: "</tt><tt class="py-op">,</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt id="link-473" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-473', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"num_hsps_attempted_gapping_in_prelim_test"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-comment"># Number of HSP's gapped (non-prelim): 291</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt id="link-474" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-474', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"Number of HSP's gapped (non-prelim): "</tt><tt class="py-op">,</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt id="link-475" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-475', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"num_hsps_gapped"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"><tt class="py-comment"># frameshift window, decay const: 50, 0.1</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-476" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.frameshift_info=Bio.expressions.blast.ncbiblast-module.html#frameshift_info"><a title="Bio.expressions.blast.ncbiblast.frameshift_info" class="py-name" href="#" onclick="return doclink('link-476', 'frameshift_info', 'link-476');">frameshift_info</a></tt> <tt class="py-op">=</tt> <tt id="link-477" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-477', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"frameshift window, decay const: "</tt><tt class="py-op">,</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt id="link-478" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-478', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"frameshift_window"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt id="link-479" class="py-name"><a title="Martel.Re" class="py-name" href="#" onclick="return doclink('link-479', 'Re', 'link-13');">Re</a></tt><tt class="py-op">(</tt><tt class="py-string">r", *"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt id="link-480" class="py-name"><a title="Bio.expressions.blast.ncbiblast.float_stat" class="py-name" href="#" onclick="return doclink('link-480', 'float_stat', 'link-406');">float_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"frameshift_decat_const"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> </tt>
<a name="_bit_info"></a><div id="_bit_info-def"><a name="L414"></a><tt class="py-lineno">414</tt> <a class="py-toggle" href="#" id="_bit_info-toggle" onclick="return toggle('_bit_info');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.expressions.blast.ncbiblast-module.html#_bit_info">_bit_info</a><tt class="py-op">(</tt><tt class="py-param">s</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_bit_info-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_bit_info-expanded"><a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-481" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-481', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt id="link-482" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-482', 's', 'link-355');">s</a></tt><tt class="py-op">,</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt id="link-483" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-483', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt id="link-484" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-484', 'name', 'link-85');">name</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt id="link-485" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-485', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-486" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-486', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">"("</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-487" class="py-name"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-487', 'Opt', 'link-4');">Opt</a></tt><tt class="py-op">(</tt><tt id="link-488" class="py-name"><a title="Martel.Spaces" class="py-name" href="#" onclick="return doclink('link-488', 'Spaces', 'link-5');">Spaces</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt id="link-489" class="py-name"><a title="Bio.expressions.blast.ncbiblast.float_stat" class="py-name" href="#" onclick="return doclink('link-489', 'float_stat', 'link-406');">float_stat</a></tt><tt class="py-op">(</tt><tt id="link-490" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-490', 'name', 'link-85');">name</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"_bits"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt id="link-491" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-491', 'Str', 'link-8');">Str</a></tt><tt class="py-op">(</tt><tt class="py-string">" bits)"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-comment"># T: 0</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-492" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.t_info=Bio.expressions.blast.ncbiblast-module.html#t_info"><a title="Bio.expressions.blast.ncbiblast.t_info" class="py-name" href="#" onclick="return doclink('link-492', 't_info', 'link-492');">t_info</a></tt> <tt class="py-op">=</tt> <tt id="link-493" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-493', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"T: "</tt><tt class="py-op">,</tt> <tt id="link-494" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-494', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"t"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-comment"># A: 0</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-495" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.a_info=Bio.expressions.blast.ncbiblast-module.html#a_info"><a title="Bio.expressions.blast.ncbiblast.a_info" class="py-name" href="#" onclick="return doclink('link-495', 'a_info', 'link-495');">a_info</a></tt> <tt class="py-op">=</tt> <tt id="link-496" class="py-name"><a title="Bio.expressions.blast.ncbiblast._nv" class="py-name" href="#" onclick="return doclink('link-496', '_nv', 'link-432');">_nv</a></tt><tt class="py-op">(</tt><tt class="py-string">"A: "</tt><tt class="py-op">,</tt> <tt id="link-497" class="py-name"><a title="Bio.expressions.blast.ncbiblast.int_stat" class="py-name" href="#" onclick="return doclink('link-497', 'int_stat', 'link-443');">int_stat</a></tt><tt class="py-op">(</tt><tt class="py-string">"1"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-comment"># X1: 6 (11.9 bits)</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-498" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.x1_info=Bio.expressions.blast.ncbiblast-module.html#x1_info"><a title="Bio.expressions.blast.ncbiblast.x1_info" class="py-name" href="#" onclick="return doclink('link-498', 'x1_info', 'link-498');">x1_info</a></tt> <tt class="py-op">=</tt> <tt id="link-499" class="py-name" targets="Function Bio.expressions.blast.ncbiblast._bit_info()=Bio.expressions.blast.ncbiblast-module.html#_bit_info"><a title="Bio.expressions.blast.ncbiblast._bit_info" class="py-name" href="#" onclick="return doclink('link-499', '_bit_info', 'link-499');">_bit_info</a></tt><tt class="py-op">(</tt><tt class="py-string">"X1: "</tt><tt class="py-op">,</tt> <tt class="py-string">"x1"</tt><tt class="py-op">)</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt class="py-comment"># X2: 10 (19.8 bits)</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-500" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.x2_info=Bio.expressions.blast.ncbiblast-module.html#x2_info"><a title="Bio.expressions.blast.ncbiblast.x2_info" class="py-name" href="#" onclick="return doclink('link-500', 'x2_info', 'link-500');">x2_info</a></tt> <tt class="py-op">=</tt> <tt id="link-501" class="py-name"><a title="Bio.expressions.blast.ncbiblast._bit_info" class="py-name" href="#" onclick="return doclink('link-501', '_bit_info', 'link-499');">_bit_info</a></tt><tt class="py-op">(</tt><tt class="py-string">"X2: "</tt><tt class="py-op">,</tt> <tt class="py-string">"x2"</tt><tt class="py-op">)</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-comment"># X3: 64 (24.9 bits)</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-502" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.x3_info=Bio.expressions.blast.ncbiblast-module.html#x3_info"><a title="Bio.expressions.blast.ncbiblast.x3_info" class="py-name" href="#" onclick="return doclink('link-502', 'x3_info', 'link-502');">x3_info</a></tt> <tt class="py-op">=</tt> <tt id="link-503" class="py-name"><a title="Bio.expressions.blast.ncbiblast._bit_info" class="py-name" href="#" onclick="return doclink('link-503', '_bit_info', 'link-499');">_bit_info</a></tt><tt class="py-op">(</tt><tt class="py-string">"X3: "</tt><tt class="py-op">,</tt> <tt class="py-string">"x3"</tt><tt class="py-op">)</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt class="py-comment"># S1: 12 (24.3 bits)</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-504" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.s1_info=Bio.expressions.blast.ncbiblast-module.html#s1_info"><a title="Bio.expressions.blast.ncbiblast.s1_info" class="py-name" href="#" onclick="return doclink('link-504', 's1_info', 'link-504');">s1_info</a></tt> <tt class="py-op">=</tt> <tt id="link-505" class="py-name"><a title="Bio.expressions.blast.ncbiblast._bit_info" class="py-name" href="#" onclick="return doclink('link-505', '_bit_info', 'link-499');">_bit_info</a></tt><tt class="py-op">(</tt><tt class="py-string">"S1: "</tt><tt class="py-op">,</tt> <tt class="py-string">"s1"</tt><tt class="py-op">)</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt class="py-comment"># S2: 19 (38.2 bits)</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-506" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.s2_info=Bio.expressions.blast.ncbiblast-module.html#s2_info"><a title="Bio.expressions.blast.ncbiblast.s2_info" class="py-name" href="#" onclick="return doclink('link-506', 's2_info', 'link-506');">s2_info</a></tt> <tt class="py-op">=</tt> <tt id="link-507" class="py-name"><a title="Bio.expressions.blast.ncbiblast._bit_info" class="py-name" href="#" onclick="return doclink('link-507', '_bit_info', 'link-499');">_bit_info</a></tt><tt class="py-op">(</tt><tt class="py-string">"S2: "</tt><tt class="py-op">,</tt> <tt class="py-string">"s2"</tt><tt class="py-op">)</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"><tt id="link-508" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastn_ending=Bio.expressions.blast.ncbiblast-module.html#blastn_ending,Variable Bio.expressions.blast.wublast.blastn_ending=Bio.expressions.blast.wublast-module.html#blastn_ending"><a title="Bio.expressions.blast.ncbiblast.blastn_ending
Bio.expressions.blast.wublast.blastn_ending" class="py-name" href="#" onclick="return doclink('link-508', 'blastn_ending', 'link-508');">blastn_ending</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-509" class="py-name"><a title="Bio.expressions.blast.ncbiblast.db_stats" class="py-name" href="#" onclick="return doclink('link-509', 'db_stats', 'link-392');">db_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt id="link-510" class="py-name"><a title="Bio.expressions.blast.ncbiblast.lambda_stats" class="py-name" href="#" onclick="return doclink('link-510', 'lambda_stats', 'link-425');">lambda_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> <tt id="link-511" class="py-name"><a title="Bio.expressions.blast.ncbiblast.matrix_stats" class="py-name" href="#" onclick="return doclink('link-511', 'matrix_stats', 'link-429');">matrix_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt id="link-512" class="py-name"><a title="Bio.expressions.blast.ncbiblast.gap_penalties_stats" class="py-name" href="#" onclick="return doclink('link-512', 'gap_penalties_stats', 'link-436');">gap_penalties_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> <tt id="link-513" class="py-name"><a title="Bio.expressions.blast.ncbiblast.generic_info1" class="py-name" href="#" onclick="return doclink('link-513', 'generic_info1', 'link-441');">generic_info1</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt id="link-514" class="py-name"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-514', 'Opt', 'link-4');">Opt</a></tt><tt class="py-op">(</tt><tt id="link-515" class="py-name"><a title="Bio.expressions.blast.ncbiblast.hsp_info" class="py-name" href="#" onclick="return doclink('link-515', 'hsp_info', 'link-467');">hsp_info</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt id="link-516" class="py-name"><a title="Bio.expressions.blast.ncbiblast.generic_info2" class="py-name" href="#" onclick="return doclink('link-516', 'generic_info2', 'link-452');">generic_info2</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt id="link-517" class="py-name"><a title="Bio.expressions.blast.ncbiblast.t_info" class="py-name" href="#" onclick="return doclink('link-517', 't_info', 'link-492');">t_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt id="link-518" class="py-name"><a title="Bio.expressions.blast.ncbiblast.a_info" class="py-name" href="#" onclick="return doclink('link-518', 'a_info', 'link-495');">a_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> <tt id="link-519" class="py-name"><a title="Bio.expressions.blast.ncbiblast.x1_info" class="py-name" href="#" onclick="return doclink('link-519', 'x1_info', 'link-498');">x1_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> <tt id="link-520" class="py-name"><a title="Bio.expressions.blast.ncbiblast.x2_info" class="py-name" href="#" onclick="return doclink('link-520', 'x2_info', 'link-500');">x2_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> <tt id="link-521" class="py-name"><a title="Bio.expressions.blast.ncbiblast.s1_info" class="py-name" href="#" onclick="return doclink('link-521', 's1_info', 'link-504');">s1_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> <tt id="link-522" class="py-name"><a title="Bio.expressions.blast.ncbiblast.s2_info" class="py-name" href="#" onclick="return doclink('link-522', 's2_info', 'link-506');">s2_info</a></tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"><tt id="link-523" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastp_ending=Bio.expressions.blast.ncbiblast-module.html#blastp_ending,Variable Bio.expressions.blast.wublast.blastp_ending=Bio.expressions.blast.wublast-module.html#blastp_ending"><a title="Bio.expressions.blast.ncbiblast.blastp_ending
Bio.expressions.blast.wublast.blastp_ending" class="py-name" href="#" onclick="return doclink('link-523', 'blastp_ending', 'link-523');">blastp_ending</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-524" class="py-name"><a title="Bio.expressions.blast.ncbiblast.db_stats" class="py-name" href="#" onclick="return doclink('link-524', 'db_stats', 'link-392');">db_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt id="link-525" class="py-name"><a title="Bio.expressions.blast.ncbiblast.lambda_stats" class="py-name" href="#" onclick="return doclink('link-525', 'lambda_stats', 'link-425');">lambda_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> <tt id="link-526" class="py-name"><a title="Bio.expressions.blast.ncbiblast.matrix_stats" class="py-name" href="#" onclick="return doclink('link-526', 'matrix_stats', 'link-429');">matrix_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> <tt id="link-527" class="py-name"><a title="Bio.expressions.blast.ncbiblast.gap_penalties_stats" class="py-name" href="#" onclick="return doclink('link-527', 'gap_penalties_stats', 'link-436');">gap_penalties_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt id="link-528" class="py-name"><a title="Bio.expressions.blast.ncbiblast.generic_info1" class="py-name" href="#" onclick="return doclink('link-528', 'generic_info1', 'link-441');">generic_info1</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> <tt id="link-529" class="py-name"><a title="Bio.expressions.blast.ncbiblast.hsp_info" class="py-name" href="#" onclick="return doclink('link-529', 'hsp_info', 'link-467');">hsp_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt id="link-530" class="py-name"><a title="Bio.expressions.blast.ncbiblast.generic_info2" class="py-name" href="#" onclick="return doclink('link-530', 'generic_info2', 'link-452');">generic_info2</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt id="link-531" class="py-name"><a title="Bio.expressions.blast.ncbiblast.t_info" class="py-name" href="#" onclick="return doclink('link-531', 't_info', 'link-492');">t_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt id="link-532" class="py-name"><a title="Bio.expressions.blast.ncbiblast.a_info" class="py-name" href="#" onclick="return doclink('link-532', 'a_info', 'link-495');">a_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt id="link-533" class="py-name"><a title="Bio.expressions.blast.ncbiblast.x1_info" class="py-name" href="#" onclick="return doclink('link-533', 'x1_info', 'link-498');">x1_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt id="link-534" class="py-name"><a title="Bio.expressions.blast.ncbiblast.x2_info" class="py-name" href="#" onclick="return doclink('link-534', 'x2_info', 'link-500');">x2_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt id="link-535" class="py-name"><a title="Bio.expressions.blast.ncbiblast.x3_info" class="py-name" href="#" onclick="return doclink('link-535', 'x3_info', 'link-502');">x3_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt id="link-536" class="py-name"><a title="Bio.expressions.blast.ncbiblast.s1_info" class="py-name" href="#" onclick="return doclink('link-536', 's1_info', 'link-504');">s1_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt id="link-537" class="py-name"><a title="Bio.expressions.blast.ncbiblast.s2_info" class="py-name" href="#" onclick="return doclink('link-537', 's2_info', 'link-506');">s2_info</a></tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"><tt id="link-538" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastx_ending=Bio.expressions.blast.ncbiblast-module.html#blastx_ending,Variable Bio.expressions.blast.wublast.blastx_ending=Bio.expressions.blast.wublast-module.html#blastx_ending"><a title="Bio.expressions.blast.ncbiblast.blastx_ending
Bio.expressions.blast.wublast.blastx_ending" class="py-name" href="#" onclick="return doclink('link-538', 'blastx_ending', 'link-538');">blastx_ending</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-539" class="py-name"><a title="Bio.expressions.blast.ncbiblast.db_stats" class="py-name" href="#" onclick="return doclink('link-539', 'db_stats', 'link-392');">db_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt id="link-540" class="py-name"><a title="Bio.expressions.blast.ncbiblast.lambda_stats" class="py-name" href="#" onclick="return doclink('link-540', 'lambda_stats', 'link-425');">lambda_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt id="link-541" class="py-name"><a title="Bio.expressions.blast.ncbiblast.matrix_stats" class="py-name" href="#" onclick="return doclink('link-541', 'matrix_stats', 'link-429');">matrix_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt id="link-542" class="py-name"><a title="Bio.expressions.blast.ncbiblast.gap_penalties_stats" class="py-name" href="#" onclick="return doclink('link-542', 'gap_penalties_stats', 'link-436');">gap_penalties_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt id="link-543" class="py-name"><a title="Bio.expressions.blast.ncbiblast.generic_info1" class="py-name" href="#" onclick="return doclink('link-543', 'generic_info1', 'link-441');">generic_info1</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt id="link-544" class="py-name"><a title="Bio.expressions.blast.ncbiblast.hsp_info" class="py-name" href="#" onclick="return doclink('link-544', 'hsp_info', 'link-467');">hsp_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt id="link-545" class="py-name"><a title="Bio.expressions.blast.ncbiblast.generic_info2" class="py-name" href="#" onclick="return doclink('link-545', 'generic_info2', 'link-452');">generic_info2</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt id="link-546" class="py-name"><a title="Bio.expressions.blast.ncbiblast.frameshift_info" class="py-name" href="#" onclick="return doclink('link-546', 'frameshift_info', 'link-476');">frameshift_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt id="link-547" class="py-name"><a title="Bio.expressions.blast.ncbiblast.t_info" class="py-name" href="#" onclick="return doclink('link-547', 't_info', 'link-492');">t_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt id="link-548" class="py-name"><a title="Bio.expressions.blast.ncbiblast.a_info" class="py-name" href="#" onclick="return doclink('link-548', 'a_info', 'link-495');">a_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt id="link-549" class="py-name"><a title="Bio.expressions.blast.ncbiblast.x1_info" class="py-name" href="#" onclick="return doclink('link-549', 'x1_info', 'link-498');">x1_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt id="link-550" class="py-name"><a title="Bio.expressions.blast.ncbiblast.x2_info" class="py-name" href="#" onclick="return doclink('link-550', 'x2_info', 'link-500');">x2_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt id="link-551" class="py-name"><a title="Bio.expressions.blast.ncbiblast.x3_info" class="py-name" href="#" onclick="return doclink('link-551', 'x3_info', 'link-502');">x3_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt id="link-552" class="py-name"><a title="Bio.expressions.blast.ncbiblast.s1_info" class="py-name" href="#" onclick="return doclink('link-552', 's1_info', 'link-504');">s1_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt id="link-553" class="py-name"><a title="Bio.expressions.blast.ncbiblast.s2_info" class="py-name" href="#" onclick="return doclink('link-553', 's2_info', 'link-506');">s2_info</a></tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"><tt id="link-554" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.tblastn_ending=Bio.expressions.blast.ncbiblast-module.html#tblastn_ending"><a title="Bio.expressions.blast.ncbiblast.tblastn_ending" class="py-name" href="#" onclick="return doclink('link-554', 'tblastn_ending', 'link-554');">tblastn_ending</a></tt> <tt class="py-op">=</tt> <tt id="link-555" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastx_ending
Bio.expressions.blast.wublast.blastx_ending" class="py-name" href="#" onclick="return doclink('link-555', 'blastx_ending', 'link-538');">blastx_ending</a></tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"><tt id="link-556" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.tblastx_ending=Bio.expressions.blast.ncbiblast-module.html#tblastx_ending"><a title="Bio.expressions.blast.ncbiblast.tblastx_ending" class="py-name" href="#" onclick="return doclink('link-556', 'tblastx_ending', 'link-556');">tblastx_ending</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-557" class="py-name"><a title="Bio.expressions.blast.ncbiblast.db_stats" class="py-name" href="#" onclick="return doclink('link-557', 'db_stats', 'link-392');">db_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt id="link-558" class="py-name"><a title="Bio.expressions.blast.ncbiblast.ungapped_lambda_stats" class="py-name" href="#" onclick="return doclink('link-558', 'ungapped_lambda_stats', 'link-402');">ungapped_lambda_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> <tt id="link-559" class="py-name"><a title="Bio.expressions.blast.ncbiblast.matrix_stats" class="py-name" href="#" onclick="return doclink('link-559', 'matrix_stats', 'link-429');">matrix_stats</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"> <tt id="link-560" class="py-name"><a title="Bio.expressions.blast.ncbiblast.generic_info1" class="py-name" href="#" onclick="return doclink('link-560', 'generic_info1', 'link-441');">generic_info1</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> <tt id="link-561" class="py-name"><a title="Bio.expressions.blast.ncbiblast.generic_info2" class="py-name" href="#" onclick="return doclink('link-561', 'generic_info2', 'link-452');">generic_info2</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt id="link-562" class="py-name"><a title="Bio.expressions.blast.ncbiblast.frameshift_info" class="py-name" href="#" onclick="return doclink('link-562', 'frameshift_info', 'link-476');">frameshift_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> <tt id="link-563" class="py-name"><a title="Bio.expressions.blast.ncbiblast.t_info" class="py-name" href="#" onclick="return doclink('link-563', 't_info', 'link-492');">t_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> <tt id="link-564" class="py-name"><a title="Bio.expressions.blast.ncbiblast.a_info" class="py-name" href="#" onclick="return doclink('link-564', 'a_info', 'link-495');">a_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt id="link-565" class="py-name"><a title="Bio.expressions.blast.ncbiblast.x1_info" class="py-name" href="#" onclick="return doclink('link-565', 'x1_info', 'link-498');">x1_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt id="link-566" class="py-name"><a title="Bio.expressions.blast.ncbiblast.x2_info" class="py-name" href="#" onclick="return doclink('link-566', 'x2_info', 'link-500');">x2_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt id="link-567" class="py-name"><a title="Bio.expressions.blast.ncbiblast.s1_info" class="py-name" href="#" onclick="return doclink('link-567', 's1_info', 'link-504');">s1_info</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt id="link-568" class="py-name"><a title="Bio.expressions.blast.ncbiblast.s2_info" class="py-name" href="#" onclick="return doclink('link-568', 's2_info', 'link-506');">s2_info</a></tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"><tt id="link-569" class="py-name" targets="Method Bio.Restriction.Restriction.RestrictionBatch.format()=Bio.Restriction.Restriction.RestrictionBatch-class.html#format,Variable Bio.expressions.blast.ncbiblast.format=Bio.expressions.blast.ncbiblast-module.html#format,Variable Bio.expressions.blast.wublast.format=Bio.expressions.blast.wublast-module.html#format,Variable Bio.expressions.blocks.format=Bio.expressions.blocks-module.html#format,Variable Bio.expressions.embl.embl65.format=Bio.expressions.embl.embl65-module.html#format,Variable Bio.expressions.fasta.format=Bio.expressions.fasta-module.html#format,Variable Bio.expressions.genbank.format=Bio.expressions.genbank-module.html#format,Variable Bio.expressions.hmmpfam.format=Bio.expressions.hmmpfam-module.html#format,Variable Bio.expressions.swissprot.ipi.format=Bio.expressions.swissprot.ipi-module.html#format,Variable Bio.expressions.swissprot.speclist.format=Bio.expressions.swissprot.speclist-module.html#format,Variable Bio.expressions.swissprot.sprot38.format=Bio.expressions.swissprot.sprot38-module.html#format,Variable Bio.expressions.swissprot.sprot40.format=Bio.expressions.swissprot.sprot40-module.html#format,Variable Bio.expressions.transfac.format=Bio.expressions.transfac-module.html#format,Variable Martel.test.test_swissprot38.format=Martel.test.test_swissprot38-module.html#format,Variable Martel.test.testformats.swissprot38.format=Martel.test.testformats.swissprot38-module.html#format"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-569', 'format', 'link-569');">format</a></tt> <tt class="py-op">=</tt> <tt id="link-570" class="py-name"><a title="Bio.Std" class="py-name" href="#" onclick="return doclink('link-570', 'Std', 'link-2');">Std</a></tt><tt class="py-op">.</tt><tt id="link-571" class="py-name" targets="Variable Bio.Emboss.primer3_format.record=Bio.Emboss.primer3_format-module.html#record,Variable Bio.Emboss.primersearch_format.record=Bio.Emboss.primersearch_format-module.html#record,Method Bio.GFF.Feature.record()=Bio.GFF.Feature-class.html#record,Variable Bio.LocusLink.web_parse.record=Bio.LocusLink.web_parse-module.html#record,Variable Bio.Ndb.record=Bio.Ndb-module.html#record,Function Bio.Std.record()=Bio.Std-module.html#record,Variable Bio.expressions.blocks.record=Bio.expressions.blocks-module.html#record,Variable Bio.expressions.embl.embl65.record=Bio.expressions.embl.embl65-module.html#record,Variable Bio.expressions.fasta.record=Bio.expressions.fasta-module.html#record,Variable Bio.expressions.genbank.record=Bio.expressions.genbank-module.html#record,Variable Bio.expressions.hmmpfam.record=Bio.expressions.hmmpfam-module.html#record,Variable Bio.expressions.swissprot.ipi.record=Bio.expressions.swissprot.ipi-module.html#record,Variable Bio.expressions.swissprot.speclist.record=Bio.expressions.swissprot.speclist-module.html#record,Variable Bio.expressions.swissprot.sprot38.record=Bio.expressions.swissprot.sprot38-module.html#record,Variable Bio.expressions.swissprot.sprot40.record=Bio.expressions.swissprot.sprot40-module.html#record,Variable Martel.test.test_swissprot38.record=Martel.test.test_swissprot38-module.html#record,Variable Martel.test.testformats.swissprot38.record=Martel.test.testformats.swissprot38-module.html#record"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-571', 'record', 'link-571');">record</a></tt><tt class="py-op">(</tt><tt id="link-572" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-572', 'Group', 'link-12');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"appheader"</tt><tt class="py-op">,</tt> <tt id="link-573" class="py-name"><a title="Martel.Expression.NullOp" class="py-name" href="#" onclick="return doclink('link-573', 'NullOp', 'link-154');">NullOp</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt id="link-574" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-574', 'header', 'link-145');">header</a></tt> <tt class="py-op">+</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt id="link-575" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-575', 'Rep', 'link-72');">Rep</a></tt><tt class="py-op">(</tt><tt id="link-576" class="py-name"><a title="Bio.Std.hit
Bio.expressions.blast.ncbiblast.hit" class="py-name" href="#" onclick="return doclink('link-576', 'hit', 'link-346');">hit</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt id="link-577" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-577', 'Group', 'link-12');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"ending"</tt><tt class="py-op">,</tt> <tt id="link-578" class="py-name"><a title="Martel.Expression.NullOp" class="py-name" href="#" onclick="return doclink('link-578', 'NullOp', 'link-154');">NullOp</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"><tt id="link-579" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastn=Bio.expressions.blast.ncbiblast-module.html#blastn,Variable Bio.expressions.blast.wublast.blastn=Bio.expressions.blast.wublast-module.html#blastn,Variable Bio.formatdefs.search.blastn=Bio.formatdefs.search-module.html#blastn"><a title="Bio.expressions.blast.ncbiblast.blastn
Bio.expressions.blast.wublast.blastn
Bio.formatdefs.search.blastn" class="py-name" href="#" onclick="return doclink('link-579', 'blastn', 'link-579');">blastn</a></tt> <tt class="py-op">=</tt> <tt id="link-580" class="py-name" targets="Function Martel.replace_groups()=Martel-module.html#replace_groups"><a title="Martel.replace_groups" class="py-name" href="#" onclick="return doclink('link-580', 'replace_groups', 'link-580');">replace_groups</a></tt><tt class="py-op">(</tt><tt id="link-581" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-581', 'format', 'link-569');">format</a></tt><tt class="py-op">,</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">"appheader"</tt><tt class="py-op">,</tt> <tt id="link-582" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastn_appheader
Bio.expressions.blast.wublast.blastn_appheader" class="py-name" href="#" onclick="return doclink('link-582', 'blastn_appheader', 'link-14');">blastn_appheader</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"hsp_header"</tt><tt class="py-op">,</tt> <tt id="link-583" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastn_hsp_header
Bio.expressions.blast.wublast.blastn_hsp_header" class="py-name" href="#" onclick="return doclink('link-583', 'blastn_hsp_header', 'link-305');">blastn_hsp_header</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"ending"</tt><tt class="py-op">,</tt> <tt id="link-584" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastn_ending
Bio.expressions.blast.wublast.blastn_ending" class="py-name" href="#" onclick="return doclink('link-584', 'blastn_ending', 'link-508');">blastn_ending</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"><tt id="link-585" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastp=Bio.expressions.blast.ncbiblast-module.html#blastp,Variable Bio.expressions.blast.wublast.blastp=Bio.expressions.blast.wublast-module.html#blastp,Variable Bio.formatdefs.search.blastp=Bio.formatdefs.search-module.html#blastp"><a title="Bio.expressions.blast.ncbiblast.blastp
Bio.expressions.blast.wublast.blastp
Bio.formatdefs.search.blastp" class="py-name" href="#" onclick="return doclink('link-585', 'blastp', 'link-585');">blastp</a></tt> <tt class="py-op">=</tt> <tt id="link-586" class="py-name"><a title="Martel.replace_groups" class="py-name" href="#" onclick="return doclink('link-586', 'replace_groups', 'link-580');">replace_groups</a></tt><tt class="py-op">(</tt><tt id="link-587" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-587', 'format', 'link-569');">format</a></tt><tt class="py-op">,</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">"appheader"</tt><tt class="py-op">,</tt> <tt id="link-588" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastp_appheader
Bio.expressions.blast.wublast.blastp_appheader" class="py-name" href="#" onclick="return doclink('link-588', 'blastp_appheader', 'link-22');">blastp_appheader</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"hsp_header"</tt><tt class="py-op">,</tt> <tt id="link-589" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastp_hsp_header
Bio.expressions.blast.wublast.blastp_hsp_header" class="py-name" href="#" onclick="return doclink('link-589', 'blastp_hsp_header', 'link-311');">blastp_hsp_header</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"ending"</tt><tt class="py-op">,</tt> <tt id="link-590" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastp_ending
Bio.expressions.blast.wublast.blastp_ending" class="py-name" href="#" onclick="return doclink('link-590', 'blastp_ending', 'link-523');">blastp_ending</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"><tt id="link-591" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastx=Bio.expressions.blast.ncbiblast-module.html#blastx,Variable Bio.expressions.blast.wublast.blastx=Bio.expressions.blast.wublast-module.html#blastx,Variable Bio.formatdefs.search.blastx=Bio.formatdefs.search-module.html#blastx"><a title="Bio.expressions.blast.ncbiblast.blastx
Bio.expressions.blast.wublast.blastx
Bio.formatdefs.search.blastx" class="py-name" href="#" onclick="return doclink('link-591', 'blastx', 'link-591');">blastx</a></tt> <tt class="py-op">=</tt> <tt id="link-592" class="py-name"><a title="Martel.replace_groups" class="py-name" href="#" onclick="return doclink('link-592', 'replace_groups', 'link-580');">replace_groups</a></tt><tt class="py-op">(</tt><tt id="link-593" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-593', 'format', 'link-569');">format</a></tt><tt class="py-op">,</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">"appheader"</tt><tt class="py-op">,</tt> <tt id="link-594" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastx_appheader
Bio.expressions.blast.wublast.blastx_appheader" class="py-name" href="#" onclick="return doclink('link-594', 'blastx_appheader', 'link-30');">blastx_appheader</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"hsp_header"</tt><tt class="py-op">,</tt> <tt id="link-595" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastx_hsp_header
Bio.expressions.blast.wublast.blastx_hsp_header" class="py-name" href="#" onclick="return doclink('link-595', 'blastx_hsp_header', 'link-315');">blastx_hsp_header</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"ending"</tt><tt class="py-op">,</tt> <tt id="link-596" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastx_ending
Bio.expressions.blast.wublast.blastx_ending" class="py-name" href="#" onclick="return doclink('link-596', 'blastx_ending', 'link-538');">blastx_ending</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"><tt id="link-597" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.tblastn=Bio.expressions.blast.ncbiblast-module.html#tblastn,Variable Bio.expressions.blast.wublast.tblastn=Bio.expressions.blast.wublast-module.html#tblastn,Variable Bio.formatdefs.search.tblastn=Bio.formatdefs.search-module.html#tblastn"><a title="Bio.expressions.blast.ncbiblast.tblastn
Bio.expressions.blast.wublast.tblastn
Bio.formatdefs.search.tblastn" class="py-name" href="#" onclick="return doclink('link-597', 'tblastn', 'link-597');">tblastn</a></tt> <tt class="py-op">=</tt> <tt id="link-598" class="py-name"><a title="Martel.replace_groups" class="py-name" href="#" onclick="return doclink('link-598', 'replace_groups', 'link-580');">replace_groups</a></tt><tt class="py-op">(</tt><tt id="link-599" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-599', 'format', 'link-569');">format</a></tt><tt class="py-op">,</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">"appheader"</tt><tt class="py-op">,</tt> <tt id="link-600" class="py-name"><a title="Bio.expressions.blast.ncbiblast.tblastn_appheader
Bio.expressions.blast.wublast.tblastn_appheader" class="py-name" href="#" onclick="return doclink('link-600', 'tblastn_appheader', 'link-38');">tblastn_appheader</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"hsp_header"</tt><tt class="py-op">,</tt> <tt id="link-601" class="py-name"><a title="Bio.expressions.blast.ncbiblast.tblastn_hsp_header
Bio.expressions.blast.wublast.tblastn_hsp_header" class="py-name" href="#" onclick="return doclink('link-601', 'tblastn_hsp_header', 'link-320');">tblastn_hsp_header</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"ending"</tt><tt class="py-op">,</tt> <tt id="link-602" class="py-name"><a title="Bio.expressions.blast.ncbiblast.tblastn_ending" class="py-name" href="#" onclick="return doclink('link-602', 'tblastn_ending', 'link-554');">tblastn_ending</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"><tt id="link-603" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.tblastx=Bio.expressions.blast.ncbiblast-module.html#tblastx,Variable Bio.formatdefs.search.tblastx=Bio.formatdefs.search-module.html#tblastx"><a title="Bio.expressions.blast.ncbiblast.tblastx
Bio.formatdefs.search.tblastx" class="py-name" href="#" onclick="return doclink('link-603', 'tblastx', 'link-603');">tblastx</a></tt> <tt class="py-op">=</tt> <tt id="link-604" class="py-name"><a title="Martel.replace_groups" class="py-name" href="#" onclick="return doclink('link-604', 'replace_groups', 'link-580');">replace_groups</a></tt><tt class="py-op">(</tt><tt id="link-605" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-605', 'format', 'link-569');">format</a></tt><tt class="py-op">,</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">"appheader"</tt><tt class="py-op">,</tt> <tt id="link-606" class="py-name"><a title="Bio.expressions.blast.ncbiblast.tblastx_appheader
Bio.expressions.blast.wublast.tblastx_appheader" class="py-name" href="#" onclick="return doclink('link-606', 'tblastx_appheader', 'link-46');">tblastx_appheader</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"hsp_header"</tt><tt class="py-op">,</tt> <tt id="link-607" class="py-name"><a title="Bio.expressions.blast.ncbiblast.tblastx_hsp_header" class="py-name" href="#" onclick="return doclink('link-607', 'tblastx_hsp_header', 'link-325');">tblastx_hsp_header</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"ending"</tt><tt class="py-op">,</tt> <tt id="link-608" class="py-name"><a title="Bio.expressions.blast.ncbiblast.tblastx_ending" class="py-name" href="#" onclick="return doclink('link-608', 'tblastx_ending', 'link-556');">tblastx_ending</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> </tt><script type="text/javascript">
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