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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Saf-module.html">Package Saf</a> ::
Module saf_format
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<h1 class="epydoc">Source Code for <a href="Bio.Saf.saf_format-module.html">Module Bio.Saf.saf_format</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2001 by Katharine Lindner. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""Martel based parser to read SAF formatted files.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">This is a huge regular regular expression for SAF, built using</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">the 'regular expressiona on steroids' capabilities of Martel.</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring">http://www.embl-heidelberg.de/predictprotein/Dexa/optin_safDes.html</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-docstring">Notes:</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-docstring">Just so I remember -- the new end of line syntax is:</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-docstring"> New regexp syntax - \R</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring"> \R means "\n|\r\n?"</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring"> [\R] means "[\n\r]"</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring">This helps us have endlines be consistent across platforms.</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-comment">#http://www.embl-heidelberg.de/predictprotein/Dexa/optin_safDes.html</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-comment"># Martel</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</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>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-1', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" 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-2', 'Str', 'link-2');">Str</a></tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-3', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" 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-4', 'AnyEol', 'link-4');">AnyEol</a></tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-5', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Function Martel.ToEol()=Martel-module.html#ToEol"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-6', 'ToEol', 'link-6');">ToEol</a></tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-7" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-7', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" 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-8', 'Group', 'link-8');">Group</a></tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-9" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-9', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-10" class="py-name" targets="Function Martel.Alt()=Martel-module.html#Alt,Class Martel.Expression.Alt=Martel.Expression.Alt-class.html"><a title="Martel.Alt
Martel.Expression.Alt" class="py-name" href="#" onclick="return doclink('link-10', 'Alt', 'link-10');">Alt</a></tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-11" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-11', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-12" 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-12', 'Rep', 'link-12');">Rep</a></tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-13" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-13', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-14" class="py-name" targets="Function Martel.Rep1()=Martel-module.html#Rep1"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-14', 'Rep1', 'link-14');">Rep1</a></tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-15" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-15', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-16" class="py-name" targets="Function Martel.Any()=Martel-module.html#Any,Class Martel.Expression.Any=Martel.Expression.Any-class.html"><a title="Martel.Any
Martel.Expression.Any" class="py-name" href="#" onclick="return doclink('link-16', 'Any', 'link-16');">Any</a></tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-17" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-17', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-18" class="py-name" targets="Function Martel.Opt()=Martel-module.html#Opt"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-18', 'Opt', 'link-18');">Opt</a></tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-19" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-19', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-20" class="py-name" targets="Function Martel.ToSep()=Martel-module.html#ToSep"><a title="Martel.ToSep" class="py-name" href="#" onclick="return doclink('link-20', 'ToSep', 'link-20');">ToSep</a></tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-21" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-21', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Class Bio.EUtils.Datatypes.Expression=Bio.EUtils.Datatypes.Expression-class.html,Module Martel.Expression=Martel.Expression-module.html,Class Martel.Expression.Expression=Martel.Expression.Expression-class.html"><a title="Bio.EUtils.Datatypes.Expression
Martel.Expression
Martel.Expression.Expression" class="py-name" href="#" onclick="return doclink('link-22', 'Expression', 'link-22');">Expression</a></tt> <tt class="py-keyword">import</tt> <tt id="link-23" 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-23', 'Assert', 'link-23');">Assert</a></tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"><tt class="py-comment"># --- first set up some helper constants and functions</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Copyright 2001 by Katharine Lindner. All rights reserved.</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"><tt id="link-24" class="py-name" targets="Variable Bio.MetaTool.metatool_format.digits=Bio.MetaTool.metatool_format-module.html#digits,Variable Bio.Saf.saf_format.digits=Bio.Saf.saf_format-module.html#digits"><a title="Bio.MetaTool.metatool_format.digits
Bio.Saf.saf_format.digits" class="py-name" href="#" onclick="return doclink('link-24', 'digits', 'link-24');">digits</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"0123456789"</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"><tt id="link-25" class="py-name" targets="Variable Bio.Saf.saf_format.valid_sequence_characters=Bio.Saf.saf_format-module.html#valid_sequence_characters"><a title="Bio.Saf.saf_format.valid_sequence_characters" class="py-name" href="#" onclick="return doclink('link-25', 'valid_sequence_characters', 'link-25');">valid_sequence_characters</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ-. \t'</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"><tt id="link-26" class="py-name" targets="Variable Bio.CDD.cdd_format.white_space=Bio.CDD.cdd_format-module.html#white_space,Variable Bio.LocusLink.locus_format.white_space=Bio.LocusLink.locus_format-module.html#white_space,Variable Bio.MetaTool.metatool_format.white_space=Bio.MetaTool.metatool_format-module.html#white_space,Variable Bio.Saf.saf_format.white_space=Bio.Saf.saf_format-module.html#white_space"><a title="Bio.CDD.cdd_format.white_space
Bio.LocusLink.locus_format.white_space
Bio.MetaTool.metatool_format.white_space
Bio.Saf.saf_format.white_space" class="py-name" href="#" onclick="return doclink('link-26', 'white_space', 'link-26');">white_space</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"\t "</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"><tt id="link-27" class="py-name" targets="Variable Bio.Saf.saf_format.valid_residue_characters=Bio.Saf.saf_format-module.html#valid_residue_characters"><a title="Bio.Saf.saf_format.valid_residue_characters" class="py-name" href="#" onclick="return doclink('link-27', 'valid_residue_characters', 'link-27');">valid_residue_characters</a></tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="Bio.MetaTool.metatool_format.digits
Bio.Saf.saf_format.digits" class="py-name" href="#" onclick="return doclink('link-28', 'digits', 'link-24');">digits</a></tt> <tt class="py-op">+</tt> <tt id="link-29" class="py-name"><a title="Bio.CDD.cdd_format.white_space
Bio.LocusLink.locus_format.white_space
Bio.MetaTool.metatool_format.white_space
Bio.Saf.saf_format.white_space" class="py-name" href="#" onclick="return doclink('link-29', 'white_space', 'link-26');">white_space</a></tt> <tt class="py-op">+</tt> <tt class="py-name">chr</tt><tt class="py-op">(</tt> <tt class="py-number">0x2e</tt> <tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"><tt id="link-30" class="py-name" targets="Variable Bio.Saf.saf_format.residue_number_line=Bio.Saf.saf_format-module.html#residue_number_line"><a title="Bio.Saf.saf_format.residue_number_line" class="py-name" href="#" onclick="return doclink('link-30', 'residue_number_line', 'link-30');">residue_number_line</a></tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-31', 'Group', 'link-8');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"residue_number_line"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt id="link-32" class="py-name"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-32', 'Rep1', 'link-14');">Rep1</a></tt><tt class="py-op">(</tt> <tt id="link-33" class="py-name"><a title="Martel.Any
Martel.Expression.Any" class="py-name" href="#" onclick="return doclink('link-33', 'Any', 'link-16');">Any</a></tt><tt class="py-op">(</tt> <tt id="link-34" class="py-name"><a title="Bio.Saf.saf_format.valid_residue_characters" class="py-name" href="#" onclick="return doclink('link-34', 'valid_residue_characters', 'link-27');">valid_residue_characters</a></tt> <tt class="py-op">)</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-35" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-35', 'AnyEol', 'link-4');">AnyEol</a></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-36" class="py-name" targets="Variable Bio.Emboss.primer3_format.comment_line=Bio.Emboss.primer3_format-module.html#comment_line,Variable Bio.IntelliGenetics.intelligenetics_format.comment_line=Bio.IntelliGenetics.intelligenetics_format-module.html#comment_line,Variable Bio.NBRF.nbrf_format.comment_line=Bio.NBRF.nbrf_format-module.html#comment_line,Variable Bio.Saf.saf_format.comment_line=Bio.Saf.saf_format-module.html#comment_line"><a title="Bio.Emboss.primer3_format.comment_line
Bio.IntelliGenetics.intelligenetics_format.comment_line
Bio.NBRF.nbrf_format.comment_line
Bio.Saf.saf_format.comment_line" class="py-name" href="#" onclick="return doclink('link-36', 'comment_line', 'link-36');">comment_line</a></tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-37', 'Group', 'link-8');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"comment_line"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt id="link-38" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-38', 'Str', 'link-2');">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="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> <tt id="link-39" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-39', 'ToEol', 'link-6');">ToEol</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 id="link-40" class="py-name" targets="Variable Bio.Saf.saf_format.ignored_line=Bio.Saf.saf_format-module.html#ignored_line"><a title="Bio.Saf.saf_format.ignored_line" class="py-name" href="#" onclick="return doclink('link-40', 'ignored_line', 'link-40');">ignored_line</a></tt> <tt class="py-op">=</tt> <tt id="link-41" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-41', 'Group', 'link-8');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"ignored_line"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt id="link-42" class="py-name"><a title="Martel.Alt
Martel.Expression.Alt" class="py-name" href="#" onclick="return doclink('link-42', 'Alt', 'link-10');">Alt</a></tt><tt class="py-op">(</tt> <tt id="link-43" class="py-name"><a title="Bio.Emboss.primer3_format.comment_line
Bio.IntelliGenetics.intelligenetics_format.comment_line
Bio.NBRF.nbrf_format.comment_line
Bio.Saf.saf_format.comment_line" class="py-name" href="#" onclick="return doclink('link-43', 'comment_line', 'link-36');">comment_line</a></tt><tt class="py-op">,</tt> <tt id="link-44" class="py-name"><a title="Bio.Saf.saf_format.residue_number_line" class="py-name" href="#" onclick="return doclink('link-44', 'residue_number_line', 'link-30');">residue_number_line</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"><tt id="link-45" class="py-name" targets="Variable Bio.Saf.saf_format.candidate_line=Bio.Saf.saf_format-module.html#candidate_line"><a title="Bio.Saf.saf_format.candidate_line" class="py-name" href="#" onclick="return doclink('link-45', 'candidate_line', 'link-45');">candidate_line</a></tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-46', 'Group', 'link-8');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"candidate_line"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt id="link-47" class="py-name"><a title="Martel.Assert
Martel.Expression.Assert" class="py-name" href="#" onclick="return doclink('link-47', 'Assert', 'link-23');">Assert</a></tt><tt class="py-op">(</tt> <tt id="link-48" class="py-name"><a title="Martel.Expression.Str
Martel.Str" class="py-name" href="#" onclick="return doclink('link-48', 'Str', 'link-2');">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-number">1</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-49" class="py-name"><a title="Martel.Assert
Martel.Expression.Assert" class="py-name" href="#" onclick="return doclink('link-49', 'Assert', 'link-23');">Assert</a></tt><tt class="py-op">(</tt> <tt id="link-50" class="py-name"><a title="Martel.Any
Martel.Expression.Any" class="py-name" href="#" onclick="return doclink('link-50', 'Any', 'link-16');">Any</a></tt><tt class="py-op">(</tt> <tt id="link-51" class="py-name"><a title="Bio.Saf.saf_format.valid_residue_characters" class="py-name" href="#" onclick="return doclink('link-51', 'valid_residue_characters', 'link-27');">valid_residue_characters</a></tt> <tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">1</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-52" class="py-name"><a title="Martel.ToSep" class="py-name" href="#" onclick="return doclink('link-52', 'ToSep', 'link-20');">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="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> <tt id="link-53" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-53', 'Rep', 'link-12');">Rep</a></tt><tt class="py-op">(</tt> <tt id="link-54" class="py-name"><a title="Martel.Any
Martel.Expression.Any" class="py-name" href="#" onclick="return doclink('link-54', 'Any', 'link-16');">Any</a></tt><tt class="py-op">(</tt> <tt id="link-55" class="py-name"><a title="Bio.Saf.saf_format.valid_sequence_characters" class="py-name" href="#" onclick="return doclink('link-55', 'valid_sequence_characters', 'link-25');">valid_sequence_characters</a></tt> <tt class="py-op">)</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-56" class="py-name"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-56', 'ToEol', 'link-6');">ToEol</a></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-57" class="py-name" targets="Variable Bio.Saf.saf_format.saf_record=Bio.Saf.saf_format-module.html#saf_record"><a title="Bio.Saf.saf_format.saf_record" class="py-name" href="#" onclick="return doclink('link-57', 'saf_record', 'link-57');">saf_record</a></tt> <tt class="py-op">=</tt> <tt id="link-58" class="py-name"><a title="Martel.Expression.Group
Martel.Group" class="py-name" href="#" onclick="return doclink('link-58', 'Group', 'link-8');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"saf_record"</tt><tt class="py-op">,</tt> \ </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt id="link-59" class="py-name"><a title="Bio.Saf.saf_format.candidate_line" class="py-name" href="#" onclick="return doclink('link-59', 'candidate_line', 'link-45');">candidate_line</a></tt> <tt class="py-op">+</tt> <tt id="link-60" class="py-name"><a title="Bio.Pathway.Rep
Martel.Rep" class="py-name" href="#" onclick="return doclink('link-60', 'Rep', 'link-12');">Rep</a></tt><tt class="py-op">(</tt> <tt id="link-61" class="py-name"><a title="Martel.Alt
Martel.Expression.Alt" class="py-name" href="#" onclick="return doclink('link-61', 'Alt', 'link-10');">Alt</a></tt><tt class="py-op">(</tt> <tt id="link-62" class="py-name"><a title="Bio.Saf.saf_format.candidate_line" class="py-name" href="#" onclick="return doclink('link-62', 'candidate_line', 'link-45');">candidate_line</a></tt><tt class="py-op">,</tt> <tt id="link-63" class="py-name"><a title="Bio.Saf.saf_format.ignored_line" class="py-name" href="#" onclick="return doclink('link-63', 'ignored_line', 'link-40');">ignored_line</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-64" class="py-name"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-64', 'Opt', 'link-18');">Opt</a></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-2');">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-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> </tt><script type="text/javascript">
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