Sophie: biopython-doc-1.47-2mdv2008.1 x86

biopython-doc-1.47-2mdv2008.1.x86_64.rpm

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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
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<h1 class="epydoc">Source Code for <a href="Bio.formatdefs.search-module.html">Module Bio.formatdefs.search</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><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="Package Bio.config=Bio.config-module.html"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-1', 'config', 'link-1');">config</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.config.FormatRegistry=Bio.config.FormatRegistry-module.html,Class Bio.config.FormatRegistry.FormatRegistry=Bio.config.FormatRegistry.FormatRegistry-class.html"><a title="Bio.config.FormatRegistry
Bio.config.FormatRegistry.FormatRegistry" class="py-name" href="#" onclick="return doclink('link-2', 'FormatRegistry', 'link-2');">FormatRegistry</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.config.FormatRegistry.FormatObject=Bio.config.FormatRegistry.FormatObject-class.html"><a title="Bio.config.FormatRegistry.FormatObject" class="py-name" href="#" onclick="return doclink('link-3', 'FormatObject', 'link-3');">FormatObject</a></tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name" targets="Class Bio.config.FormatRegistry.FormatGroup=Bio.config.FormatRegistry.FormatGroup-class.html"><a title="Bio.config.FormatRegistry.FormatGroup" class="py-name" href="#" onclick="return doclink('link-4', 'FormatGroup', 'link-4');">FormatGroup</a></tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt id="link-5" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsClient.search()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#search,Method Bio.EUtils.HistoryClient.HistoryClient.search()=Bio.EUtils.HistoryClient.HistoryClient-class.html#search,Method Bio.KDTree.KDTree.KDTree.search()=Bio.KDTree.KDTree.KDTree-class.html#search,Method Bio.PDB.NeighborSearch.NeighborSearch.search()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#search,Method Bio.Prosite.Pattern.Prosite.search()=Bio.Prosite.Pattern.Prosite-class.html#search,Class Method Bio.Restriction.Restriction.AbstractCut.search()=Bio.Restriction.Restriction.AbstractCut-class.html#search,Method Bio.Restriction.Restriction.RestrictionBatch.search()=Bio.Restriction.Restriction.RestrictionBatch-class.html#search,Function Bio.SCOP.search()=Bio.SCOP-module.html#search,Module Bio.builders.Search.search=Bio.builders.Search.search-module.html,Module Bio.formatdefs.search=Bio.formatdefs.search-module.html,Variable Bio.formatdefs.search.search=Bio.formatdefs.search-module.html#search"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-5', 'search', 'link-5');">search</a></tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name"><a title="Bio.config.FormatRegistry.FormatGroup" class="py-name" href="#" onclick="return doclink('link-6', 'FormatGroup', 'link-4');">FormatGroup</a></tt><tt class="py-op">(</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line">    <tt id="link-7" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-7', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"search"</tt><tt class="py-op">,</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line">    <tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt id="link-8" class="py-name" targets="Package Bio.expressions.blast=Bio.expressions.blast-module.html,Variable Bio.formatdefs.search.blast=Bio.formatdefs.search-module.html#blast"><a title="Bio.expressions.blast
Bio.formatdefs.search.blast" class="py-name" href="#" onclick="return doclink('link-8', 'blast', 'link-8');">blast</a></tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name"><a title="Bio.config.FormatRegistry.FormatGroup" class="py-name" href="#" onclick="return doclink('link-9', 'FormatGroup', 'link-4');">FormatGroup</a></tt><tt class="py-op">(</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line">    <tt id="link-10" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-10', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"blast"</tt><tt class="py-op">,</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line">    <tt id="link-11" class="py-name" targets="Function Bio.FSSP.FSSPTools.filter()=Bio.FSSP.FSSPTools-module.html#filter,Method Bio.FilteredReader.FilteredReader.filter()=Bio.FilteredReader.FilteredReader-class.html#filter,Variable Bio.expressions.swissprot.filter=Bio.expressions.swissprot-module.html#filter"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-11', 'filter', 'link-11');">filter</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.ncbiblast.blast_filter"</tt><tt class="py-op">,</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line">    <tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt id="link-12" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-12', 'search', 'link-5');">search</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Variable Bio.Affy.CelFile.add=Bio.Affy.CelFile-module.html#add,Method Bio.EUtils.POM.ElementNode.add()=Bio.EUtils.POM.ElementNode-class.html#add,Method Bio.GFF.easy.Location.add()=Bio.GFF.easy.Location-class.html#add,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.add()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add,Variable Bio.LogisticRegression.add=Bio.LogisticRegression-module.html#add,Variable Bio.MarkovModel.add=Bio.MarkovModel-module.html#add,Variable Bio.MaxEntropy.add=Bio.MaxEntropy-module.html#add,Variable Bio.NaiveBayes.add=Bio.NaiveBayes-module.html#add,Method Bio.Nexus.Nexus.StepMatrix.add()=Bio.Nexus.Nexus.StepMatrix-class.html#add,Method Bio.Nexus.Nodes.Chain.add()=Bio.Nexus.Nodes.Chain-class.html#add,Method Bio.PDB.Entity.Entity.add()=Bio.PDB.Entity.Entity-class.html#add,Method Bio.PDB.Residue.DisorderedResidue.add()=Bio.PDB.Residue.DisorderedResidue-class.html#add,Method Bio.PDB.Residue.Residue.add()=Bio.PDB.Residue.Residue-class.html#add,Method Bio.Pathway.Rep.HashSet.HashSet.add()=Bio.Pathway.Rep.HashSet.HashSet-class.html#add,Method Bio.Restriction.Restriction.RestrictionBatch.add()=Bio.Restriction.Restriction.RestrictionBatch-class.html#add,Variable Bio.Statistics.lowess.add=Bio.Statistics.lowess-module.html#add,Method Bio.config.FormatRegistry.FormatGroup.add()=Bio.config.FormatRegistry.FormatGroup-class.html#add,Method Bio.config.Registry.RegisterableGroup.add()=Bio.config.Registry.RegisterableGroup-class.html#add,Variable Bio.distance.add=Bio.distance-module.html#add,Variable Bio.kNN.add=Bio.kNN-module.html#add,Method Martel.Dispatch.MulticallEnd.add()=Martel.Dispatch.MulticallEnd-class.html#add,Method Martel.Dispatch.MulticallStart.add()=Martel.Dispatch.MulticallStart-class.html#add"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-13', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="Bio.expressions.blast
Bio.formatdefs.search.blast" class="py-name" href="#" onclick="return doclink('link-14', 'blast', 'link-8');">blast</a></tt><tt class="py-op">)</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt id="link-15" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastp=Bio.expressions.blast.ncbiblast-module.html#blastp,Variable Bio.expressions.blast.wublast.blastp=Bio.expressions.blast.wublast-module.html#blastp,Variable Bio.formatdefs.search.blastp=Bio.formatdefs.search-module.html#blastp"><a title="Bio.expressions.blast.ncbiblast.blastp
Bio.expressions.blast.wublast.blastp
Bio.formatdefs.search.blastp" class="py-name" href="#" onclick="return doclink('link-15', 'blastp', 'link-15');">blastp</a></tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Bio.config.FormatRegistry.FormatGroup" class="py-name" href="#" onclick="return doclink('link-16', 'FormatGroup', 'link-4');">FormatGroup</a></tt><tt class="py-op">(</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line">    <tt id="link-17" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-17', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"blastp"</tt><tt class="py-op">,</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line">    <tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt id="link-18" class="py-name"><a title="Bio.expressions.blast
Bio.formatdefs.search.blast" class="py-name" href="#" onclick="return doclink('link-18', 'blast', 'link-8');">blast</a></tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-19', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastp
Bio.expressions.blast.wublast.blastp
Bio.formatdefs.search.blastp" class="py-name" href="#" onclick="return doclink('link-20', 'blastp', 'link-15');">blastp</a></tt><tt class="py-op">)</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt id="link-21" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastn=Bio.expressions.blast.ncbiblast-module.html#blastn,Variable Bio.expressions.blast.wublast.blastn=Bio.expressions.blast.wublast-module.html#blastn,Variable Bio.formatdefs.search.blastn=Bio.formatdefs.search-module.html#blastn"><a title="Bio.expressions.blast.ncbiblast.blastn
Bio.expressions.blast.wublast.blastn
Bio.formatdefs.search.blastn" class="py-name" href="#" onclick="return doclink('link-21', 'blastn', 'link-21');">blastn</a></tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="Bio.config.FormatRegistry.FormatGroup" class="py-name" href="#" onclick="return doclink('link-22', 'FormatGroup', 'link-4');">FormatGroup</a></tt><tt class="py-op">(</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line">    <tt id="link-23" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-23', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"blastn"</tt><tt class="py-op">,</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line">    <tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt id="link-24" class="py-name"><a title="Bio.expressions.blast
Bio.formatdefs.search.blast" class="py-name" href="#" onclick="return doclink('link-24', 'blast', 'link-8');">blast</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-25', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-26" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastn
Bio.expressions.blast.wublast.blastn
Bio.formatdefs.search.blastn" class="py-name" href="#" onclick="return doclink('link-26', 'blastn', 'link-21');">blastn</a></tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt id="link-27" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.blastx=Bio.expressions.blast.ncbiblast-module.html#blastx,Variable Bio.expressions.blast.wublast.blastx=Bio.expressions.blast.wublast-module.html#blastx,Variable Bio.formatdefs.search.blastx=Bio.formatdefs.search-module.html#blastx"><a title="Bio.expressions.blast.ncbiblast.blastx
Bio.expressions.blast.wublast.blastx
Bio.formatdefs.search.blastx" class="py-name" href="#" onclick="return doclink('link-27', 'blastx', 'link-27');">blastx</a></tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="Bio.config.FormatRegistry.FormatGroup" class="py-name" href="#" onclick="return doclink('link-28', 'FormatGroup', 'link-4');">FormatGroup</a></tt><tt class="py-op">(</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">    <tt id="link-29" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-29', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"blastx"</tt><tt class="py-op">,</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">    <tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt id="link-30" class="py-name"><a title="Bio.expressions.blast
Bio.formatdefs.search.blast" class="py-name" href="#" onclick="return doclink('link-30', 'blast', 'link-8');">blast</a></tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-31', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-32" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastx
Bio.expressions.blast.wublast.blastx
Bio.formatdefs.search.blastx" class="py-name" href="#" onclick="return doclink('link-32', 'blastx', 'link-27');">blastx</a></tt><tt class="py-op">)</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt id="link-33" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.tblastn=Bio.expressions.blast.ncbiblast-module.html#tblastn,Variable Bio.expressions.blast.wublast.tblastn=Bio.expressions.blast.wublast-module.html#tblastn,Variable Bio.formatdefs.search.tblastn=Bio.formatdefs.search-module.html#tblastn"><a title="Bio.expressions.blast.ncbiblast.tblastn
Bio.expressions.blast.wublast.tblastn
Bio.formatdefs.search.tblastn" class="py-name" href="#" onclick="return doclink('link-33', 'tblastn', 'link-33');">tblastn</a></tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="Bio.config.FormatRegistry.FormatGroup" class="py-name" href="#" onclick="return doclink('link-34', 'FormatGroup', 'link-4');">FormatGroup</a></tt><tt class="py-op">(</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">    <tt id="link-35" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-35', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"tblastn"</tt><tt class="py-op">,</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">    <tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line"><tt id="link-36" class="py-name"><a title="Bio.expressions.blast
Bio.formatdefs.search.blast" class="py-name" href="#" onclick="return doclink('link-36', 'blast', 'link-8');">blast</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-37', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Bio.expressions.blast.ncbiblast.tblastn
Bio.expressions.blast.wublast.tblastn
Bio.formatdefs.search.tblastn" class="py-name" href="#" onclick="return doclink('link-38', 'tblastn', 'link-33');">tblastn</a></tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"><tt id="link-39" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.tblastx=Bio.expressions.blast.ncbiblast-module.html#tblastx,Variable Bio.formatdefs.search.tblastx=Bio.formatdefs.search-module.html#tblastx"><a title="Bio.expressions.blast.ncbiblast.tblastx
Bio.formatdefs.search.tblastx" class="py-name" href="#" onclick="return doclink('link-39', 'tblastx', 'link-39');">tblastx</a></tt> <tt class="py-op">=</tt> <tt id="link-40" class="py-name"><a title="Bio.config.FormatRegistry.FormatGroup" class="py-name" href="#" onclick="return doclink('link-40', 'FormatGroup', 'link-4');">FormatGroup</a></tt><tt class="py-op">(</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">    <tt id="link-41" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-41', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"tblastx"</tt><tt class="py-op">,</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">    <tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt id="link-42" class="py-name"><a title="Bio.expressions.blast
Bio.formatdefs.search.blast" class="py-name" href="#" onclick="return doclink('link-42', 'blast', 'link-8');">blast</a></tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-43', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-44" class="py-name"><a title="Bio.expressions.blast.ncbiblast.tblastx
Bio.formatdefs.search.tblastx" class="py-name" href="#" onclick="return doclink('link-44', 'tblastx', 'link-39');">tblastx</a></tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-comment">### NCBI BLASTs</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-45" class="py-name" targets="Variable Bio.formatdefs.search.ncbi_blastp=Bio.formatdefs.search-module.html#ncbi_blastp"><a title="Bio.formatdefs.search.ncbi_blastp" class="py-name" href="#" onclick="return doclink('link-45', 'ncbi_blastp', 'link-45');">ncbi_blastp</a></tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject" class="py-name" href="#" onclick="return doclink('link-46', 'FormatObject', 'link-3');">FormatObject</a></tt><tt class="py-op">(</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">    <tt id="link-47" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-47', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"ncbi-blastp"</tt><tt class="py-op">,</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">    <tt class="py-name">abbrev</tt> <tt class="py-op">=</tt> <tt class="py-string">"ncbi_blastp"</tt><tt class="py-op">,</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">    <tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.ncbiblast.blastp"</tt><tt class="py-op">,</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">    <tt id="link-48" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-48', 'filter', 'link-11');">filter</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.ncbiblast.blastp_appheader"</tt><tt class="py-op">,</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">    <tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"><tt id="link-49" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastp
Bio.expressions.blast.wublast.blastp
Bio.formatdefs.search.blastp" class="py-name" href="#" onclick="return doclink('link-49', 'blastp', 'link-15');">blastp</a></tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-50', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-51" class="py-name"><a title="Bio.formatdefs.search.ncbi_blastp" class="py-name" href="#" onclick="return doclink('link-51', 'ncbi_blastp', 'link-45');">ncbi_blastp</a></tt><tt class="py-op">)</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"><tt id="link-52" class="py-name" targets="Variable Bio.formatdefs.search.ncbi_blastn=Bio.formatdefs.search-module.html#ncbi_blastn"><a title="Bio.formatdefs.search.ncbi_blastn" class="py-name" href="#" onclick="return doclink('link-52', 'ncbi_blastn', 'link-52');">ncbi_blastn</a></tt> <tt class="py-op">=</tt> <tt id="link-53" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject" class="py-name" href="#" onclick="return doclink('link-53', 'FormatObject', 'link-3');">FormatObject</a></tt><tt class="py-op">(</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">    <tt id="link-54" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-54', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"ncbi-blastn"</tt><tt class="py-op">,</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">    <tt class="py-name">abbrev</tt> <tt class="py-op">=</tt> <tt class="py-string">"ncbi_blastn"</tt><tt class="py-op">,</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">    <tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.ncbiblast.blastn"</tt><tt class="py-op">,</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">    <tt id="link-55" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-55', 'filter', 'link-11');">filter</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.ncbiblast.blastn_appheader"</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">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"><tt id="link-56" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastn
Bio.expressions.blast.wublast.blastn
Bio.formatdefs.search.blastn" class="py-name" href="#" onclick="return doclink('link-56', 'blastn', 'link-21');">blastn</a></tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-57', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-58" class="py-name"><a title="Bio.formatdefs.search.ncbi_blastn" class="py-name" href="#" onclick="return doclink('link-58', 'ncbi_blastn', 'link-52');">ncbi_blastn</a></tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"><tt id="link-59" class="py-name" targets="Variable Bio.formatdefs.search.ncbi_blastx=Bio.formatdefs.search-module.html#ncbi_blastx"><a title="Bio.formatdefs.search.ncbi_blastx" class="py-name" href="#" onclick="return doclink('link-59', 'ncbi_blastx', 'link-59');">ncbi_blastx</a></tt> <tt class="py-op">=</tt> <tt id="link-60" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject" class="py-name" href="#" onclick="return doclink('link-60', 'FormatObject', 'link-3');">FormatObject</a></tt><tt class="py-op">(</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">    <tt id="link-61" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-61', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"ncbi-blastx"</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">abbrev</tt> <tt class="py-op">=</tt> <tt class="py-string">"ncbi_blastx"</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">expression</tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.ncbiblast.blastx"</tt><tt class="py-op">,</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">    <tt id="link-62" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-62', 'filter', 'link-11');">filter</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.ncbiblast.blastx_appheader"</tt><tt class="py-op">,</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">    <tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line"><tt id="link-63" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastx
Bio.expressions.blast.wublast.blastx
Bio.formatdefs.search.blastx" class="py-name" href="#" onclick="return doclink('link-63', 'blastx', 'link-27');">blastx</a></tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-64', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="Bio.formatdefs.search.ncbi_blastx" class="py-name" href="#" onclick="return doclink('link-65', 'ncbi_blastx', 'link-59');">ncbi_blastx</a></tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt id="link-66" class="py-name" targets="Variable Bio.formatdefs.search.ncbi_tblastn=Bio.formatdefs.search-module.html#ncbi_tblastn"><a title="Bio.formatdefs.search.ncbi_tblastn" class="py-name" href="#" onclick="return doclink('link-66', 'ncbi_tblastn', 'link-66');">ncbi_tblastn</a></tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject" class="py-name" href="#" onclick="return doclink('link-67', 'FormatObject', 'link-3');">FormatObject</a></tt><tt class="py-op">(</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">    <tt id="link-68" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-68', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"ncbi-tblastn"</tt><tt class="py-op">,</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">    <tt class="py-name">abbrev</tt> <tt class="py-op">=</tt> <tt class="py-string">"ncbi_tblastn"</tt><tt class="py-op">,</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">    <tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.ncbiblast.tblastn"</tt><tt class="py-op">,</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">    <tt id="link-69" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-69', 'filter', 'link-11');">filter</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.ncbiblast.tblastn_appheader"</tt><tt class="py-op">,</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">    <tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"><tt id="link-70" class="py-name"><a title="Bio.expressions.blast.ncbiblast.tblastn
Bio.expressions.blast.wublast.tblastn
Bio.formatdefs.search.tblastn" class="py-name" href="#" onclick="return doclink('link-70', 'tblastn', 'link-33');">tblastn</a></tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-71', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-72" class="py-name"><a title="Bio.formatdefs.search.ncbi_tblastn" class="py-name" href="#" onclick="return doclink('link-72', 'ncbi_tblastn', 'link-66');">ncbi_tblastn</a></tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"><tt id="link-73" class="py-name" targets="Variable Bio.formatdefs.search.ncbi_tblastx=Bio.formatdefs.search-module.html#ncbi_tblastx"><a title="Bio.formatdefs.search.ncbi_tblastx" class="py-name" href="#" onclick="return doclink('link-73', 'ncbi_tblastx', 'link-73');">ncbi_tblastx</a></tt> <tt class="py-op">=</tt> <tt id="link-74" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject" class="py-name" href="#" onclick="return doclink('link-74', 'FormatObject', 'link-3');">FormatObject</a></tt><tt class="py-op">(</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">    <tt id="link-75" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-75', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"ncbi-tblastx"</tt><tt class="py-op">,</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">    <tt class="py-name">abbrev</tt> <tt class="py-op">=</tt> <tt class="py-string">"ncbi_tblastx"</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">expression</tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.ncbiblast.tblastx"</tt><tt class="py-op">,</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">    <tt id="link-76" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-76', 'filter', 'link-11');">filter</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.ncbiblast.tblastx_appheader"</tt><tt class="py-op">,</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">    <tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line"><tt id="link-77" class="py-name"><a title="Bio.expressions.blast.ncbiblast.tblastx
Bio.formatdefs.search.tblastx" class="py-name" href="#" onclick="return doclink('link-77', 'tblastx', 'link-39');">tblastx</a></tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-78', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-79" class="py-name"><a title="Bio.formatdefs.search.ncbi_tblastx" class="py-name" href="#" onclick="return doclink('link-79', 'ncbi_tblastx', 'link-73');">ncbi_tblastx</a></tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line"> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line"> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"><tt class="py-comment">### WU-BLASTs</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt id="link-80" class="py-name" targets="Variable Bio.formatdefs.search.wu_blastp=Bio.formatdefs.search-module.html#wu_blastp"><a title="Bio.formatdefs.search.wu_blastp" class="py-name" href="#" onclick="return doclink('link-80', 'wu_blastp', 'link-80');">wu_blastp</a></tt> <tt class="py-op">=</tt> <tt id="link-81" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject" class="py-name" href="#" onclick="return doclink('link-81', 'FormatObject', 'link-3');">FormatObject</a></tt><tt class="py-op">(</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">    <tt id="link-82" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-82', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"wu-blastp"</tt><tt class="py-op">,</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">    <tt class="py-name">abbrev</tt> <tt class="py-op">=</tt> <tt class="py-string">"wu_blastp"</tt><tt class="py-op">,</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">    <tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.wublast.blastp"</tt><tt class="py-op">,</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">    <tt id="link-83" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-83', 'filter', 'link-11');">filter</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.wublast.blastp_appheader"</tt><tt class="py-op">,</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">    <tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line"><tt id="link-84" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastp
Bio.expressions.blast.wublast.blastp
Bio.formatdefs.search.blastp" class="py-name" href="#" onclick="return doclink('link-84', 'blastp', 'link-15');">blastp</a></tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-85', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-86" class="py-name"><a title="Bio.formatdefs.search.wu_blastp" class="py-name" href="#" onclick="return doclink('link-86', 'wu_blastp', 'link-80');">wu_blastp</a></tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"><tt id="link-87" class="py-name" targets="Variable Bio.formatdefs.search.wu_blastn=Bio.formatdefs.search-module.html#wu_blastn"><a title="Bio.formatdefs.search.wu_blastn" class="py-name" href="#" onclick="return doclink('link-87', 'wu_blastn', 'link-87');">wu_blastn</a></tt> <tt class="py-op">=</tt> <tt id="link-88" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject" class="py-name" href="#" onclick="return doclink('link-88', 'FormatObject', 'link-3');">FormatObject</a></tt><tt class="py-op">(</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">    <tt id="link-89" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-89', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"wu-blastn"</tt><tt class="py-op">,</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">    <tt class="py-name">abbrev</tt> <tt class="py-op">=</tt> <tt class="py-string">"wu_blastn"</tt><tt class="py-op">,</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">    <tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.wublast.blastn"</tt><tt class="py-op">,</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">    <tt id="link-90" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-90', 'filter', 'link-11');">filter</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.wublast.blastn_appheader"</tt><tt class="py-op">,</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">    <tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line"><tt id="link-91" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastn
Bio.expressions.blast.wublast.blastn
Bio.formatdefs.search.blastn" class="py-name" href="#" onclick="return doclink('link-91', 'blastn', 'link-21');">blastn</a></tt><tt class="py-op">.</tt><tt id="link-92" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-92', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-93" class="py-name"><a title="Bio.formatdefs.search.wu_blastn" class="py-name" href="#" onclick="return doclink('link-93', 'wu_blastn', 'link-87');">wu_blastn</a></tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line"> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line"><tt id="link-94" class="py-name" targets="Variable Bio.formatdefs.search.wu_blastx=Bio.formatdefs.search-module.html#wu_blastx"><a title="Bio.formatdefs.search.wu_blastx" class="py-name" href="#" onclick="return doclink('link-94', 'wu_blastx', 'link-94');">wu_blastx</a></tt> <tt class="py-op">=</tt> <tt id="link-95" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject" class="py-name" href="#" onclick="return doclink('link-95', 'FormatObject', 'link-3');">FormatObject</a></tt><tt class="py-op">(</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">    <tt id="link-96" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-96', 'name', 'link-7');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"wu-blastx"</tt><tt class="py-op">,</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">    <tt class="py-name">abbrev</tt> <tt class="py-op">=</tt> <tt class="py-string">"wu_blastx"</tt><tt class="py-op">,</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">    <tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.wublast.blastx"</tt><tt class="py-op">,</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">    <tt id="link-97" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-97', 'filter', 'link-11');">filter</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Bio.expressions.blast.wublast.blastx_appheader"</tt><tt class="py-op">,</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">    <tt class="py-name">multirecord</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line"><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line"><tt id="link-98" class="py-name"><a title="Bio.expressions.blast.ncbiblast.blastx
Bio.expressions.blast.wublast.blastx
Bio.formatdefs.search.blastx" class="py-name" href="#" onclick="return doclink('link-98', 'blastx', 'link-27');">blastx</a></tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-99', 'add', 'link-13');">add</a></tt><tt class="py-op">(</tt><tt id="link-100" class="py-name"><a title="Bio.formatdefs.search.wu_blastx" class="py-name" href="#" onclick="return doclink('link-100', 'wu_blastx', 'link-94');">wu_blastx</a></tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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