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Module Generic
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<h1 class="epydoc">Source Code for <a href="Bio.Align.Generic-module.html">Module Bio.Align.Generic</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">Contains classes to deal with generic sequence alignment stuff not</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">specific to a particular program or format.</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">classes:</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">o Alignment</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>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"># standard library</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"># biopython</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html,Class Martel.Expression.Seq=Martel.Expression.Seq-class.html,Function Martel.Seq()=Martel-module.html#Seq"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-1', 'Seq', 'link-1');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-2', 'Seq', 'link-1');">Seq</a></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Module Bio.SeqRecord=Bio.SeqRecord-module.html,Class Bio.SeqRecord.SeqRecord=Bio.SeqRecord.SeqRecord-class.html,Package Bio.builders.SeqRecord=Bio.builders.SeqRecord-module.html,Package Bio.writers.SeqRecord=Bio.writers.SeqRecord-module.html"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.builders.SeqRecord
Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-4', 'SeqRecord', 'link-4');">SeqRecord</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.builders.SeqRecord
Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-5', 'SeqRecord', 'link-4');">SeqRecord</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-7', 'Alphabet', 'link-7');">Alphabet</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-8" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-8', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-9', 'Alphabet', 'link-7');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-10" class="py-name" targets="Module Bio.Alphabet.IUPAC=Bio.Alphabet.IUPAC-module.html"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-10', 'IUPAC', 'link-10');">IUPAC</a></tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> </tt>
<a name="Alignment"></a><div id="Alignment-def"><a name="L18"></a><tt class="py-lineno"> 18</tt> <a class="py-toggle" href="#" id="Alignment-toggle" onclick="return toggle('Alignment');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html">Alignment</a><tt class="py-op">:</tt> </tt>
</div><div id="Alignment-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Alignment-expanded"><a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-docstring">"""Represent a set of alignments.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> This is a base class to represent alignments, which can be subclassed</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> to deal with an alignment in a specific format.</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Alignment.__init__"></a><div id="Alignment.__init__-def"><a name="L24"></a><tt class="py-lineno"> 24</tt> <a class="py-toggle" href="#" id="Alignment.__init__-toggle" onclick="return toggle('Alignment.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.__init__-expanded"><a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize a new Alignment object.</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> o alphabet - The alphabet to use for the sequence objects that are</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> created. This alphabet must be a gapped type.</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method Bio.MEME.Motif.Motif._alphabet()=Bio.MEME.Motif.Motif-class.html#_alphabet,Method Bio.MEME.Parser.MASTRecord._alphabet()=Bio.MEME.Parser.MASTRecord-class.html#_alphabet,Method Bio.MEME.Parser._MEMEConsumer._alphabet()=Bio.MEME.Parser._MEMEConsumer-class.html#_alphabet"><a title="Bio.MEME.Motif.Motif._alphabet
Bio.MEME.Parser.MASTRecord._alphabet
Bio.MEME.Parser._MEMEConsumer._alphabet" class="py-name" href="#" onclick="return doclink('link-11', '_alphabet', 'link-11');">_alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name" targets="Variable Bio.Prosite.Pattern.Prosite.alphabet=Bio.Prosite.Pattern.Prosite-class.html#alphabet,Function Bio.Std.alphabet()=Bio.Std-module.html#alphabet"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-12', 'alphabet', 'link-12');">alphabet</a></tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-comment"># hold everything at a list of seq record objects</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> </tt>
<a name="Alignment._str_line"></a><div id="Alignment._str_line-def"><a name="L35"></a><tt class="py-lineno"> 35</tt> <a class="py-toggle" href="#" id="Alignment._str_line-toggle" onclick="return toggle('Alignment._str_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#_str_line">_str_line</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Alignment._str_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment._str_line-expanded"><a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a truncated string representation of a SeqRecord.</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> This is a PRIVATE function used by the __str__ method.</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-13" 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-13', 'record', 'link-13');">record</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-14', 'seq', 'link-14');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op"><=</tt> <tt class="py-number">50</tt> <tt class="py-op">:</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"%s %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-15" class="py-name"><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-15', 'record', 'link-13');">record</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-16', 'seq', 'link-14');">seq</a></tt><tt class="py-op">,</tt> <tt id="link-17" class="py-name"><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-17', 'record', 'link-13');">record</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Variable Bio.Data.CodonTable.id=Bio.Data.CodonTable-module.html#id,Variable Bio.Encodings.IUPACEncoding.id=Bio.Encodings.IUPACEncoding-module.html#id,Method Bio.GFF.Feature.id()=Bio.GFF.Feature-class.html#id"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-18', 'id', 'link-18');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"%s...%s %s"</tt> \ </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-19" class="py-name"><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-19', 'record', 'link-13');">record</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-20', 'seq', 'link-14');">seq</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">44</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-21" class="py-name"><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-21', 'record', 'link-13');">record</a></tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-22', 'seq', 'link-14');">seq</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-23" class="py-name"><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-23', 'record', 'link-13');">record</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-24', 'id', 'link-18');">id</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> </tt>
<a name="Alignment.__str__"></a><div id="Alignment.__str__-def"><a name="L46"></a><tt class="py-lineno"> 46</tt> <a class="py-toggle" href="#" id="Alignment.__str__-toggle" onclick="return toggle('Alignment.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Alignment.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.__str__-expanded"><a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a multi-line string summary of the alignment.</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> This output is intended to be readable, but large alignments are</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> shown truncated. A maximum of 20 rows (sequences) and 50 columns</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> are shown, with the record identifiers. This should fit nicely on a</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> single screen. e.g.</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> DNAAlphabet() alignment with 3 rows and 14 columns</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> ACGATCAGCTAGCT Alpha</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> CCGATCAGCTAGCT Beta</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> ACGATGAGCTAGCT Gamma </tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">rows</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"%s alignment with %i rows and %i columns"</tt> \ </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.MEME.Motif.Motif._alphabet
Bio.MEME.Parser.MASTRecord._alphabet
Bio.MEME.Parser._MEMEConsumer._alphabet" class="py-name" href="#" onclick="return doclink('link-25', '_alphabet', 'link-11');">_alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">rows</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.Align.Generic.Alignment.get_alignment_length()=Bio.Align.Generic.Alignment-class.html#get_alignment_length"><a title="Bio.Align.Generic.Alignment.get_alignment_length" class="py-name" href="#" onclick="return doclink('link-26', 'get_alignment_length', 'link-26');">get_alignment_length</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="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rows</tt> <tt class="py-op"><=</tt> <tt class="py-number">20</tt> <tt class="py-op">:</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.extend()=Bio.EUtils.POM.ElementNode-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-27', 'extend', 'link-27');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method Bio.Align.Generic.Alignment._str_line()=Bio.Align.Generic.Alignment-class.html#_str_line"><a title="Bio.Align.Generic.Alignment._str_line" class="py-name" href="#" onclick="return doclink('link-28', '_str_line', 'link-28');">_str_line</a></tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</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 class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-29', 'extend', 'link-27');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.Align.Generic.Alignment._str_line" class="py-name" href="#" onclick="return doclink('link-30', '_str_line', 'link-28');">_str_line</a></tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">18</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 class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-31', 'append', 'link-31');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"..."</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-32', 'append', 'link-31');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Align.Generic.Alignment._str_line" class="py-name" href="#" onclick="return doclink('link-33', '_str_line', 'link-28');">_str_line</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</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 class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"\n"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">)</tt> </tt>
</div><a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="Alignment.__repr__"></a><div id="Alignment.__repr__-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="Alignment.__repr__-toggle" onclick="return toggle('Alignment.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Alignment.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.__repr__-expanded"><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a representation of the object for debugging.</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> The representation cannot be used with eval() to recreate the object,</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"> which is usually possible with simple python ojects. For example:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> <Bio.Align.Generic.Alignment instance (2 records of length 14,</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> SingleLetterAlphabet()) at a3c184c></tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> The hex string is the memory address of the object, see help(id).</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> This provides a simple way to visually distinguish alignments of</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> the same size.</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"<%s instance (%i records of length %i, %s) at %x>"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</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 class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.Align.Generic.Alignment.get_alignment_length" class="py-name" href="#" onclick="return doclink('link-34', 'get_alignment_length', 'link-26');">get_alignment_length</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.MEME.Motif.Motif._alphabet
Bio.MEME.Parser.MASTRecord._alphabet
Bio.MEME.Parser._MEMEConsumer._alphabet" class="py-name" href="#" onclick="return doclink('link-35', '_alphabet', 'link-11');">_alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-36" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-36', 'id', 'link-18');">id</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-comment">#This version is useful for doing eval(repr(alignment)),</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#but it can be VERY long:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#return "%s(%s, %s)" \</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># % (self.__class__, repr(self._records), repr(self._alphabet))</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="Alignment.get_all_seqs"></a><div id="Alignment.get_all_seqs-def"><a name="L91"></a><tt class="py-lineno"> 91</tt> <a class="py-toggle" href="#" id="Alignment.get_all_seqs-toggle" onclick="return toggle('Alignment.get_all_seqs');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#get_all_seqs">get_all_seqs</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.get_all_seqs-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.get_all_seqs-expanded"><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-docstring">"""Return all of the sequences involved in the alignment.</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> The return value is a list of SeqRecord objects.</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt> </tt>
</div><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> </tt>
<a name="Alignment.__iter__"></a><div id="Alignment.__iter__-def"><a name="L98"></a><tt class="py-lineno"> 98</tt> <a class="py-toggle" href="#" id="Alignment.__iter__-toggle" onclick="return toggle('Alignment.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#__iter__">__iter__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Alignment.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.__iter__-expanded"><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over alignment rows as SeqRecord objects</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> e.g.</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> for record in align :</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> print record.id</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> print record.seq</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">)</tt> </tt>
</div><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> </tt>
<a name="Alignment.get_seq_by_num"></a><div id="Alignment.get_seq_by_num-def"><a name="L109"></a><tt class="py-lineno">109</tt> <a class="py-toggle" href="#" id="Alignment.get_seq_by_num-toggle" onclick="return toggle('Alignment.get_seq_by_num');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#get_seq_by_num">get_seq_by_num</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">number</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.get_seq_by_num-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.get_seq_by_num-expanded"><a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-docstring">"""Retrieve a sequence by row number.</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> Returns:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> o A Seq object for the requested sequence.</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> Raises:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> o IndexError - If the specified number is out of range.</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">[</tt><tt class="py-name">number</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-37', 'seq', 'link-14');">seq</a></tt> </tt>
</div><a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> </tt>
<a name="Alignment.get_alignment_length"></a><div id="Alignment.get_alignment_length-def"><a name="L120"></a><tt class="py-lineno">120</tt> <a class="py-toggle" href="#" id="Alignment.get_alignment_length-toggle" onclick="return toggle('Alignment.get_alignment_length');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#get_alignment_length">get_alignment_length</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.get_alignment_length-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.get_alignment_length-expanded"><a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the maximum length of the alignment.</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> All objects in the alignment should (hopefully) have the same</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> length. This function will go through and find this length</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> by finding the maximum length of sequences in the alignment.</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">max_length</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-38" class="py-name"><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-38', 'record', 'link-13');">record</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-39" class="py-name"><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-39', 'record', 'link-13');">record</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-40', 'seq', 'link-14');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-name">max_length</tt><tt class="py-op">:</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">max_length</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><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-41', 'record', 'link-13');">record</a></tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-42', 'seq', 'link-14');">seq</a></tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">max_length</tt> </tt>
</div><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="Alignment.add_sequence"></a><div id="Alignment.add_sequence-def"><a name="L135"></a><tt class="py-lineno">135</tt> <a class="py-toggle" href="#" id="Alignment.add_sequence-toggle" onclick="return toggle('Alignment.add_sequence');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#add_sequence">add_sequence</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">descriptor</tt><tt class="py-op">,</tt> <tt class="py-param">sequence</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">end</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-param">weight</tt> <tt class="py-op">=</tt> <tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.add_sequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.add_sequence-expanded"><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-docstring">"""Add a sequence to the alignment.</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"> This doesn't do any kind of alignment, it just adds in the sequence</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"> object, which is assumed to be prealigned with the existing</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"> sequences.</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"> o descriptor - The descriptive id of the sequence being added.</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> This will be used as the resulting SeqRecord's</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> .id property (and, for historical compatibility,</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> also the .description property)</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> o sequence - A string with sequence info.</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"> o start - You can explicitly set the start point of the sequence.</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> This is useful (at least) for BLAST alignments, which can just</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> be partial alignments of sequences.</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> o end - Specify the end of the sequence, which is important</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> for the same reason as the start.</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"> o weight - The weight to place on the sequence in the alignment.</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"> By default, all sequences have the same weight. (0.0 => no weight,</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> 1.0 => highest weight)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">new_seq</tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-43', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt id="link-44" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-44', 'sequence', 'link-44');">sequence</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.MEME.Motif.Motif._alphabet
Bio.MEME.Parser.MASTRecord._alphabet
Bio.MEME.Parser._MEMEConsumer._alphabet" class="py-name" href="#" onclick="return doclink('link-45', '_alphabet', 'link-11');">_alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-comment">#We are now effectively using the SeqRecord's .id as</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#the primary identifier (e.g. in Bio.SeqIO) so we should</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#populate it with the descriptor.</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#For backwards compatibility, also store this in the</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#SeqRecord's description property.</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">new_record</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.builders.SeqRecord
Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-46', 'SeqRecord', 'link-4');">SeqRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">new_seq</tt><tt class="py-op">,</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt id="link-47" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-47', 'id', 'link-18');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">descriptor</tt><tt class="py-op">,</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt id="link-48" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer.description()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#description,Method Bio.Enzyme._RecordConsumer.description()=Bio.Enzyme._RecordConsumer-class.html#description,Method Bio.Prosite._RecordConsumer.description()=Bio.Prosite._RecordConsumer-class.html#description,Function Bio.Std.description()=Bio.Std-module.html#description,Method Bio.SwissProt.SProt._RecordConsumer.description()=Bio.SwissProt.SProt._RecordConsumer-class.html#description,Method Bio.SwissProt.SProt._SequenceConsumer.description()=Bio.SwissProt.SProt._SequenceConsumer-class.html#description,Variable Martel.setup.run_local_tests.description=Martel.setup.run_local_tests-class.html#description"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-48', 'description', 'link-48');">description</a></tt> <tt class="py-op">=</tt> <tt class="py-name">descriptor</tt><tt class="py-op">)</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-comment"># hack! We really need to work out how to deal with annotations</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># and features in biopython. Right now, I'll just use the</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># generic annotations dictionary we've got to store the start</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># and end, but we should think up something better. I don't know</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># if I'm really a big fan of the LocatableSeq thing they've got</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># in BioPerl, but I'm not positive what the best thing to do on</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># this is...</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-49" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-49', 'start', 'link-49');">start</a></tt><tt class="py-op">:</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">new_record</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Variable BioSQL.BioSeq.DBSeqRecord.annotations=BioSQL.BioSeq.DBSeqRecord-class.html#annotations"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-50', 'annotations', 'link-50');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">'start'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-51" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-51', 'start', 'link-49');">start</a></tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-52" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-52', 'end', 'link-52');">end</a></tt><tt class="py-op">:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">new_record</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-53', 'annotations', 'link-50');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">'end'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-54" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-54', 'end', 'link-52');">end</a></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 class="py-comment"># another hack to add weight information to the sequence</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">new_record</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-55', 'annotations', 'link-50');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">'weight'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">weight</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-56', 'append', 'link-31');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">new_record</tt><tt class="py-op">)</tt> </tt>
</div><a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt>
<a name="Alignment.get_column"></a><div id="Alignment.get_column-def"><a name="L186"></a><tt class="py-lineno">186</tt> <a class="py-toggle" href="#" id="Alignment.get_column-toggle" onclick="return toggle('Alignment.get_column');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#get_column">get_column</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">col</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.get_column-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.get_column-expanded"><a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a string containing a given column."""</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">col_str</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">col</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">col</tt> <tt class="py-op"><=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.Align.Generic.Alignment.get_alignment_length" class="py-name" href="#" onclick="return doclink('link-57', 'get_alignment_length', 'link-26');">get_alignment_length</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">:</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">col_str</tt> <tt class="py-op">+=</tt> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-58', 'seq', 'link-14');">seq</a></tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">]</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">col_str</tt> </tt>
</div></div><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt> <tt class="py-op">:</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Mini self test..."</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-name">raw_data</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"ACGATCAGCTAGCT"</tt><tt class="py-op">,</tt> <tt class="py-string">"CCGATCAGCTAGCT"</tt><tt class="py-op">,</tt> <tt class="py-string">"ACGATGAGCTAGCT"</tt><tt class="py-op">]</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt id="link-59" class="py-name" targets="Class Bio.Align.Generic.Alignment=Bio.Align.Generic.Alignment-class.html,Class Bio.Blast.Record.Alignment=Bio.Blast.Record.Alignment-class.html,Class Bio.Wise.psw.Alignment=Bio.Wise.psw.Alignment-class.html"><a title="Bio.Align.Generic.Alignment
Bio.Blast.Record.Alignment
Bio.Wise.psw.Alignment" class="py-name" href="#" onclick="return doclink('link-59', 'Alignment', 'link-59');">Alignment</a></tt><tt class="py-op">(</tt><tt id="link-60" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-60', 'Alphabet', 'link-7');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-61" class="py-name" targets="Variable Bio.Alphabet.generic_dna=Bio.Alphabet-module.html#generic_dna"><a title="Bio.Alphabet.generic_dna" class="py-name" href="#" onclick="return doclink('link-61', 'generic_dna', 'link-61');">generic_dna</a></tt><tt class="py-op">)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name" targets="Method Bio.Align.Generic.Alignment.add_sequence()=Bio.Align.Generic.Alignment-class.html#add_sequence,Method Bio.Nexus.Nexus.Nexus.add_sequence()=Bio.Nexus.Nexus.Nexus-class.html#add_sequence,Method Bio.builders.SeqRecord.sequence.BuildSeqRecord.add_sequence()=Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#add_sequence"><a title="Bio.Align.Generic.Alignment.add_sequence
Bio.Nexus.Nexus.Nexus.add_sequence
Bio.builders.SeqRecord.sequence.BuildSeqRecord.add_sequence" class="py-name" href="#" onclick="return doclink('link-62', 'add_sequence', 'link-62');">add_sequence</a></tt><tt class="py-op">(</tt><tt class="py-string">"Alpha"</tt><tt class="py-op">,</tt> <tt class="py-name">raw_data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">weight</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.Align.Generic.Alignment.add_sequence
Bio.Nexus.Nexus.Nexus.add_sequence
Bio.builders.SeqRecord.sequence.BuildSeqRecord.add_sequence" class="py-name" href="#" onclick="return doclink('link-63', 'add_sequence', 'link-62');">add_sequence</a></tt><tt class="py-op">(</tt><tt class="py-string">"Beta"</tt><tt class="py-op">,</tt> <tt class="py-name">raw_data</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="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.Align.Generic.Alignment.add_sequence
Bio.Nexus.Nexus.Nexus.add_sequence
Bio.builders.SeqRecord.sequence.BuildSeqRecord.add_sequence" class="py-name" href="#" onclick="return doclink('link-64', 'add_sequence', 'link-62');">add_sequence</a></tt><tt class="py-op">(</tt><tt class="py-string">"Gamma"</tt><tt class="py-op">,</tt> <tt class="py-name">raw_data</tt><tt class="py-op">[</tt><tt class="py-number">2</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>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"str(a):"</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"repr(a):"</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-comment">#Iterating over the rows...</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">in</tt> <tt class="py-name">a</tt> <tt class="py-op">:</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">,</tt> <tt id="link-65" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.builders.SeqRecord
Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-65', 'SeqRecord', 'link-4');">SeqRecord</a></tt><tt class="py-op">)</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">r</tt><tt class="py-op">,</tt><tt class="py-name">rec</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">a</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 class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">,</tt> <tt id="link-66" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.builders.SeqRecord
Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-66', 'SeqRecord', 'link-4');">SeqRecord</a></tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">raw_data</tt><tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-67', 'seq', 'link-14');">seq</a></tt><tt class="py-op">.</tt><tt id="link-68" class="py-name" targets="Method Bio.Crystal.Crystal.tostring()=Bio.Crystal.Crystal-class.html#tostring,Method Bio.EUtils.POM.ElementNode.tostring()=Bio.EUtils.POM.ElementNode-class.html#tostring,Method Bio.Prosite.Pattern.Prosite.tostring()=Bio.Prosite.Pattern.Prosite-class.html#tostring,Method Bio.Seq.MutableSeq.tostring()=Bio.Seq.MutableSeq-class.html#tostring,Method Bio.Seq.Seq.tostring()=Bio.Seq.Seq-class.html#tostring,Method BioSQL.BioSeq.DBSeq.tostring()=BioSQL.BioSeq.DBSeq-class.html#tostring"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-68', 'tostring', 'link-68');">tostring</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 class="py-keyword">if</tt> <tt class="py-name">r</tt><tt class="py-op">==</tt><tt class="py-number">0</tt> <tt class="py-op">:</tt> <tt class="py-keyword">assert</tt> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-69', 'annotations', 'link-50');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">'weight'</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-number">2</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Alignment iteraction as SeqRecord OK"</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> </tt><script type="text/javascript">
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