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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.Mindy-module.html">Package&nbsp;Mindy</a> ::
        Module&nbsp;BaseDB
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<h1 class="epydoc">Source Code for <a href="Bio.Mindy.BaseDB-module.html">Module Bio.Mindy.BaseDB</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-keyword">import</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>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module Bio.Mindy.compression=Bio.Mindy.compression-module.html"><a title="Bio.Mindy.compression" class="py-name" href="#" onclick="return doclink('link-1', 'compression', 'link-1');">compression</a></tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"> </tt>
<a name="_int_str"></a><div id="_int_str-def"><a name="L5"></a><tt class="py-lineno">  5</tt> <a class="py-toggle" href="#" id="_int_str-toggle" onclick="return toggle('_int_str');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB-module.html#_int_str">_int_str</a><tt class="py-op">(</tt><tt class="py-param">i</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_int_str-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_int_str-expanded"><a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line">    <tt id="link-2" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-2', 's', 'link-2');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-3" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-3', 'i', 'link-3');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt id="link-4" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-4', 's', 'link-2');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"l"</tt><tt class="py-op">:</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-5" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-5', 's', 'link-2');">s</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-6" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-6', 's', 'link-2');">s</a></tt> </tt>
</div><a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"> </tt>
<a name="WriteDB"></a><div id="WriteDB-def"><a name="L11"></a><tt class="py-lineno"> 11</tt> <a class="py-toggle" href="#" id="WriteDB-toggle" onclick="return toggle('WriteDB');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB.WriteDB-class.html">WriteDB</a><tt class="py-op">:</tt> </tt>
</div><div id="WriteDB-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="WriteDB-expanded"><a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line">    <tt class="py-comment"># Must define 'self.filename_map' mapping from filename -&gt; fileid</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># Must define 'self.fileid_info' mapping from fileid -&gt; (filename,size)</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="WriteDB.add_filename"></a><div id="WriteDB.add_filename-def"><a name="L15"></a><tt class="py-lineno"> 15</tt> <a class="py-toggle" href="#" id="WriteDB.add_filename-toggle" onclick="return toggle('WriteDB.add_filename');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB.WriteDB-class.html#add_filename">add_filename</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">filename</tt><tt class="py-op">,</tt> <tt class="py-param">size</tt><tt class="py-op">,</tt> <tt class="py-param">fileid_info</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WriteDB.add_filename-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WriteDB.add_filename-expanded"><a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line">        <tt class="py-name">fileid</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename_map</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.EUtils.MultiDict._BaseMultiDict.get()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#get,Method Bio.EUtils.POM.ElementNode.get()=Bio.EUtils.POM.ElementNode-class.html#get,Method Bio.GenBank.NCBIDictionary.get()=Bio.GenBank.NCBIDictionary-class.html#get,Method Bio.Mindy.BaseDB.DictLookup.get()=Bio.Mindy.BaseDB.DictLookup-class.html#get,Method Bio.Prosite.ExPASyDictionary.get()=Bio.Prosite.ExPASyDictionary-class.html#get,Method Bio.Prosite.Prodoc.ExPASyDictionary.get()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get,Method Bio.PubMed.Dictionary.get()=Bio.PubMed.Dictionary-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqUtils.MissingTable.get()=Bio.SeqUtils.MissingTable-class.html#get,Method Bio.SwissProt.SProt.ExPASyDictionary.get()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#get,Method Bio.config.DBRegistry.DBGroup.get()=Bio.config.DBRegistry.DBGroup-class.html#get,Method Bio.config.DBRegistry.DBObject.get()=Bio.config.DBRegistry.DBObject-class.html#get,Method Bio.config.Registry.Registry.get()=Bio.config.Registry.Registry-class.html#get,Method Martel.Parser.MartelAttributeList.get()=Martel.Parser.MartelAttributeList-class.html#get,Method Martel.msre_parse.Tokenizer.get()=Martel.msre_parse.Tokenizer-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-7', 'get', 'link-7');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">fileid</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">fileid</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line">        <tt id="link-8" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-8', 's', 'link-2');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">str</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">filename_map</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename_map</tt><tt class="py-op">[</tt><tt class="py-name">filename</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-9', 's', 'link-2');">s</a></tt>  <tt class="py-comment"># map from filename -&gt; id</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt id="link-10" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-10', 's', 'link-2');">s</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">fileid_info</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-11', 'keys', 'link-11');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"Duplicate entry! %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-12" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-12', 's', 'link-2');">s</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fileid_info</tt><tt class="py-op">[</tt><tt id="link-13" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-13', 's', 'link-2');">s</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt id="link-14" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.size()=Bio.Affy.CelFile.CelRecord-class.html#size,Variable Bio.Alphabet.Alphabet.size=Bio.Alphabet.Alphabet-class.html#size,Variable Bio.Alphabet.Reduced.HPModel.size=Bio.Alphabet.Reduced.HPModel-class.html#size,Variable Bio.Alphabet.Reduced.Murphy10.size=Bio.Alphabet.Reduced.Murphy10-class.html#size,Variable Bio.Alphabet.Reduced.Murphy15.size=Bio.Alphabet.Reduced.Murphy15-class.html#size,Variable Bio.Alphabet.Reduced.Murphy4.size=Bio.Alphabet.Reduced.Murphy4-class.html#size,Variable Bio.Alphabet.Reduced.Murphy8.size=Bio.Alphabet.Reduced.Murphy8-class.html#size,Variable Bio.Alphabet.Reduced.PC5.size=Bio.Alphabet.Reduced.PC5-class.html#size,Variable Bio.Alphabet.SingleLetterAlphabet.size=Bio.Alphabet.SingleLetterAlphabet-class.html#size,Variable Bio.Alphabet.ThreeLetterProtein.size=Bio.Alphabet.ThreeLetterProtein-class.html#size,Method Bio.GenBank._FeatureConsumer.size()=Bio.GenBank._FeatureConsumer-class.html#size,Method Bio.GenBank._RecordConsumer.size()=Bio.GenBank._RecordConsumer-class.html#size,Variable Bio.expressions.genbank.size=Bio.expressions.genbank-module.html#size"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-14', 'size', 'link-14');">size</a></tt><tt class="py-op">)</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-15" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-15', 's', 'link-2');">s</a></tt> </tt>
</div><a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"> </tt>
<a name="WriteDB.load"></a><div id="WriteDB.load-def"><a name="L25"></a><tt class="py-lineno"> 25</tt> <a class="py-toggle" href="#" id="WriteDB.load-toggle" onclick="return toggle('WriteDB.load');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB.WriteDB-class.html#load">load</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">filename</tt><tt class="py-op">,</tt> <tt class="py-param">builder</tt><tt class="py-op">,</tt> <tt class="py-param">fileid_info</tt><tt class="py-op">,</tt> <tt class="py-param">record_tag</tt> <tt class="py-op">=</tt> <tt class="py-string">"record"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WriteDB.load-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WriteDB.load-expanded"><a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line">        <tt class="py-name">formatname</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">formatname</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">        <tt id="link-16" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-16', 'size', 'link-14');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">getsize</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">        <tt class="py-name">filetag</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.Mindy.BaseDB.WriteDB.add_filename()=Bio.Mindy.BaseDB.WriteDB-class.html#add_filename"><a title="Bio.Mindy.BaseDB.WriteDB.add_filename" class="py-name" href="#" onclick="return doclink('link-17', 'add_filename', 'link-17');">add_filename</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt id="link-18" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-18', 'size', 'link-14');">size</a></tt><tt class="py-op">,</tt> <tt class="py-name">fileid_info</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">        <tt id="link-19" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.source()=Bio.GenBank._FeatureConsumer-class.html#source,Method Bio.GenBank._RecordConsumer.source()=Bio.GenBank._RecordConsumer-class.html#source,Method Bio.Medline._RecordConsumer.source()=Bio.Medline._RecordConsumer-class.html#source,Method Bio.Pathway.Network.source()=Bio.Pathway.Network-class.html#source,Method Bio.Rebase._RecordConsumer.source()=Bio.Rebase._RecordConsumer-class.html#source"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-19', 'source', 'link-19');">source</a></tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name"><a title="Bio.Mindy.compression" class="py-name" href="#" onclick="return doclink('link-20', 'compression', 'link-1');">compression</a></tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Function Bio.Mindy.compression.open_file()=Bio.Mindy.compression-module.html#open_file"><a title="Bio.Mindy.compression.open_file" class="py-name" href="#" onclick="return doclink('link-21', 'open_file', 'link-21');">open_file</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-string">"rb"</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">formatname</tt> <tt class="py-op">==</tt> <tt class="py-string">"unknown"</tt><tt class="py-op">:</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">            <tt class="py-name">formatname</tt> <tt class="py-op">=</tt> <tt class="py-string">"sequence"</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">         </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">        <tt id="link-22" class="py-name" targets="Method Bio.Restriction.Restriction.RestrictionBatch.format()=Bio.Restriction.Restriction.RestrictionBatch-class.html#format,Variable Bio.expressions.blast.ncbiblast.format=Bio.expressions.blast.ncbiblast-module.html#format,Variable Bio.expressions.blast.wublast.format=Bio.expressions.blast.wublast-module.html#format,Variable Bio.expressions.blocks.format=Bio.expressions.blocks-module.html#format,Variable Bio.expressions.embl.embl65.format=Bio.expressions.embl.embl65-module.html#format,Variable Bio.expressions.fasta.format=Bio.expressions.fasta-module.html#format,Variable Bio.expressions.genbank.format=Bio.expressions.genbank-module.html#format,Variable Bio.expressions.hmmpfam.format=Bio.expressions.hmmpfam-module.html#format,Variable Bio.expressions.swissprot.ipi.format=Bio.expressions.swissprot.ipi-module.html#format,Variable Bio.expressions.swissprot.speclist.format=Bio.expressions.swissprot.speclist-module.html#format,Variable Bio.expressions.swissprot.sprot38.format=Bio.expressions.swissprot.sprot38-module.html#format,Variable Bio.expressions.swissprot.sprot40.format=Bio.expressions.swissprot.sprot40-module.html#format,Variable Bio.expressions.transfac.format=Bio.expressions.transfac-module.html#format,Variable Martel.test.test_swissprot38.format=Martel.test.test_swissprot38-module.html#format,Variable Martel.test.testformats.swissprot38.format=Martel.test.testformats.swissprot38-module.html#format"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-22', 'format', 'link-22');">format</a></tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-23', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Variable Bio.config.FormatRegistry.formats=Bio.config.FormatRegistry-module.html#formats,Package Martel.formats=Martel.formats-module.html"><a title="Bio.config.FormatRegistry.formats
Martel.formats" class="py-name" href="#" onclick="return doclink('link-24', 'formats', 'link-24');">formats</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.normalize=Bio.EUtils.DTDs.LinkOut.normalize-class.html,Method Bio.PDB.Vector'.Vector.normalize()=Bio.PDB.Vector%27.Vector-class.html#normalize,Method Bio.config.FormatRegistry.FormatRegistry.normalize()=Bio.config.FormatRegistry.FormatRegistry-class.html#normalize,Function Martel.test.test_RecordReader2.normalize()=Martel.test.test_RecordReader2-module.html#normalize"><a title="Bio.EUtils.DTDs.LinkOut.normalize
Bio.PDB.Vector'.Vector.normalize
Bio.config.FormatRegistry.FormatRegistry.normalize
Martel.test.test_RecordReader2.normalize" class="py-name" href="#" onclick="return doclink('link-25', 'normalize', 'link-25');">normalize</a></tt><tt class="py-op">(</tt><tt class="py-name">formatname</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.config.FormatRegistry.FormatGroup.identifyFile()=Bio.config.FormatRegistry.FormatGroup-class.html#identifyFile,Method Bio.config.FormatRegistry.FormatObject.identifyFile()=Bio.config.FormatRegistry.FormatObject-class.html#identifyFile"><a title="Bio.config.FormatRegistry.FormatGroup.identifyFile
Bio.config.FormatRegistry.FormatObject.identifyFile" class="py-name" href="#" onclick="return doclink('link-26', 'identifyFile', 'link-26');">identifyFile</a></tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-27', 'source', 'link-19');">source</a></tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-28" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-28', 'format', 'link-22');">format</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot identify file as a %s format"</tt> <tt class="py-op">%</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</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">formatname</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">formatname</tt> <tt class="py-op">==</tt> <tt class="py-string">"unknown"</tt><tt class="py-op">:</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">            <tt class="py-name">expected_names</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"fasta"</tt><tt class="py-op">,</tt> <tt class="py-string">"embl"</tt><tt class="py-op">,</tt> <tt class="py-string">"swissprot"</tt><tt class="py-op">,</tt> <tt class="py-string">"genbank"</tt><tt class="py-op">]</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt id="link-29" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.node()=Bio.EUtils.POM.ElementNode-class.html#node,Method Bio.Nexus.Trees.Tree.node()=Bio.Nexus.Trees.Tree-class.html#node"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-29', 'node', 'link-29');">node</a></tt> <tt class="py-keyword">in</tt> <tt id="link-30" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-30', 'format', 'link-22');">format</a></tt><tt class="py-op">.</tt><tt class="py-name">_parents</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">if</tt> <tt id="link-31" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-31', 'node', 'link-29');">node</a></tt><tt class="py-op">.</tt><tt id="link-32" 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-32', 'name', 'link-32');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">expected_names</tt><tt class="py-op">:</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">formatname</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name"><a title="Bio.EUtils.POM.ElementNode.node
Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-33', 'node', 'link-29');">node</a></tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-34', 'name', 'link-32');">name</a></tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">                    <tt class="py-keyword">break</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">formatname</tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-35', 'format', 'link-22');">format</a></tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-36', 'name', 'link-32');">name</a></tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">         </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">        <tt class="py-name">iterator</tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-37', 'format', 'link-22');">format</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Method Bio.config.FormatRegistry.FormatObject.make_iterator()=Bio.config.FormatRegistry.FormatObject-class.html#make_iterator,Method Martel.Expression.Expression.make_iterator()=Martel.Expression.Expression-class.html#make_iterator,Method Martel.Expression.HeaderFooter.make_iterator()=Martel.Expression.HeaderFooter-class.html#make_iterator,Method Martel.Expression.ParseRecords.make_iterator()=Martel.Expression.ParseRecords-class.html#make_iterator"><a title="Bio.config.FormatRegistry.FormatObject.make_iterator
Martel.Expression.Expression.make_iterator
Martel.Expression.HeaderFooter.make_iterator
Martel.Expression.ParseRecords.make_iterator" class="py-name" href="#" onclick="return doclink('link-38', 'make_iterator', 'link-38');">make_iterator</a></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">record_tag</tt><tt class="py-op">,</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">            <tt id="link-39" class="py-name" targets="Function Martel.select_names()=Martel-module.html#select_names"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-39', 'select_names', 'link-39');">select_names</a></tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">builder</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Method Bio.Mindy.XPath.GrabXPathNodes.uses_tags()=Bio.Mindy.XPath.GrabXPathNodes-class.html#uses_tags,Method Martel.Dispatch.Dispatcher.uses_tags()=Martel.Dispatch.Dispatcher-class.html#uses_tags,Method Martel.LAX.LAX.uses_tags()=Martel.LAX.LAX-class.html#uses_tags"><a title="Bio.Mindy.XPath.GrabXPathNodes.uses_tags
Martel.Dispatch.Dispatcher.uses_tags
Martel.LAX.LAX.uses_tags" class="py-name" href="#" onclick="return doclink('link-40', 'uses_tags', 'link-40');">uses_tags</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-name">record_tag</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">            <tt class="py-name">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-41" 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-41', 'record', 'link-41');">record</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">iterator</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Method Martel.IterParser.IterHeaderFooter.iterate()=Martel.IterParser.IterHeaderFooter-class.html#iterate,Method Martel.IterParser.IterRecords.iterate()=Martel.IterParser.IterRecords-class.html#iterate,Method Martel.Iterator.Iterator.iterate()=Martel.Iterator.Iterator-class.html#iterate,Method Martel.Iterator.IteratorHeaderFooter.iterate()=Martel.Iterator.IteratorHeaderFooter-class.html#iterate,Method Martel.Iterator.IteratorRecords.iterate()=Martel.Iterator.IteratorRecords-class.html#iterate"><a title="Martel.IterParser.IterHeaderFooter.iterate
Martel.IterParser.IterRecords.iterate
Martel.Iterator.Iterator.iterate
Martel.Iterator.IteratorHeaderFooter.iterate
Martel.Iterator.IteratorRecords.iterate" class="py-name" href="#" onclick="return doclink('link-42', 'iterate', 'link-42');">iterate</a></tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-43', 'source', 'link-19');">source</a></tt><tt class="py-op">,</tt> <tt class="py-name">cont_handler</tt> <tt class="py-op">=</tt> <tt class="py-name">builder</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Method Bio.Mindy.BerkeleyDB.BerkeleyDB.add_record()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#add_record,Method Bio.Mindy.FlatDB.MemoryFlatDB.add_record()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#add_record"><a title="Bio.Mindy.BerkeleyDB.BerkeleyDB.add_record
Bio.Mindy.FlatDB.MemoryFlatDB.add_record" class="py-name" href="#" onclick="return doclink('link-44', 'add_record', 'link-44');">add_record</a></tt><tt class="py-op">(</tt><tt class="py-name">filetag</tt><tt class="py-op">,</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">                            <tt class="py-name">iterator</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt><tt class="py-op">,</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">                            <tt class="py-name">iterator</tt><tt class="py-op">.</tt><tt class="py-name">end_position</tt> <tt class="py-op">-</tt> <tt class="py-name">iterator</tt><tt class="py-op">.</tt><tt class="py-name">start_position</tt><tt class="py-op">,</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">                            <tt id="link-45" 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-45', 'record', 'link-41');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">document</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"> </tt>
<a name="DictLookup"></a><div id="DictLookup-def"><a name="L58"></a><tt class="py-lineno"> 58</tt> <a class="py-toggle" href="#" id="DictLookup-toggle" onclick="return toggle('DictLookup');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB.DictLookup-class.html">DictLookup</a><tt class="py-op">:</tt> </tt>
</div><div id="DictLookup-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DictLookup-expanded"><a name="DictLookup.__getitem__"></a><div id="DictLookup.__getitem__-def"><a name="L59"></a><tt class="py-lineno"> 59</tt> <a class="py-toggle" href="#" id="DictLookup.__getitem__-toggle" onclick="return toggle('DictLookup.__getitem__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB.DictLookup-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DictLookup.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictLookup.__getitem__-expanded"><a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-string">"Must be implemented in subclass"</tt><tt class="py-op">)</tt> </tt>
</div><a name="DictLookup.keys"></a><div id="DictLookup.keys-def"><a name="L61"></a><tt class="py-lineno"> 61</tt> <a class="py-toggle" href="#" id="DictLookup.keys-toggle" onclick="return toggle('DictLookup.keys');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB.DictLookup-class.html#keys">keys</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="DictLookup.keys-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictLookup.keys-expanded"><a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-string">"Must be implemented in subclass"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"> </tt>
<a name="DictLookup.values"></a><div id="DictLookup.values-def"><a name="L64"></a><tt class="py-lineno"> 64</tt> <a class="py-toggle" href="#" id="DictLookup.values-toggle" onclick="return toggle('DictLookup.values');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB.DictLookup-class.html#values">values</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="DictLookup.values-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictLookup.values-expanded"><a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-46" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-46', 'key', 'link-46');">key</a></tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt id="link-47" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-47', 'key', 'link-46');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-48', 'keys', 'link-11');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
</div><a name="DictLookup.items"></a><div id="DictLookup.items-def"><a name="L66"></a><tt class="py-lineno"> 66</tt> <a class="py-toggle" href="#" id="DictLookup.items-toggle" onclick="return toggle('DictLookup.items');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB.DictLookup-class.html#items">items</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="DictLookup.items-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictLookup.items-expanded"><a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-49" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-49', 'key', 'link-46');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-50" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-50', 'key', 'link-46');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-51" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-51', 'key', 'link-46');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-52', 'keys', 'link-11');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
</div><a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"> </tt>
<a name="DictLookup.get"></a><div id="DictLookup.get-def"><a name="L69"></a><tt class="py-lineno"> 69</tt> <a class="py-toggle" href="#" id="DictLookup.get-toggle" onclick="return toggle('DictLookup.get');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB.DictLookup-class.html#get">get</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">key</tt><tt class="py-op">,</tt> <tt class="py-param">default</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DictLookup.get-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictLookup.get-expanded"><a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-53" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-53', 'key', 'link-46');">key</a></tt><tt class="py-op">]</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt id="link-54" class="py-name" targets="Method Bio.Parsers.spark.GenericASTTraversal.default()=Bio.Parsers.spark.GenericASTTraversal-class.html#default"><a title="Bio.Parsers.spark.GenericASTTraversal.default" class="py-name" href="#" onclick="return doclink('link-54', 'default', 'link-54');">default</a></tt> </tt>
</div></div><a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">     </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">         </tt>
<a name="OpenDB"></a><div id="OpenDB-def"><a name="L76"></a><tt class="py-lineno"> 76</tt> <a class="py-toggle" href="#" id="OpenDB-toggle" onclick="return toggle('OpenDB');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB.OpenDB-class.html">OpenDB</a><tt class="py-op">(</tt><tt class="py-base-class">DictLookup</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="OpenDB-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="OpenDB-expanded"><a name="OpenDB.__init__"></a><div id="OpenDB.__init__-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="OpenDB.__init__-toggle" onclick="return toggle('OpenDB.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB.OpenDB-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">dbname</tt><tt class="py-op">,</tt> <tt class="py-param">index_type</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="OpenDB.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OpenDB.__init__-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbname</tt> <tt class="py-op">=</tt> <tt class="py-name">dbname</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">        <tt id="link-55" class="py-name" targets="Package Bio.config=Bio.config-module.html"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-55', 'config', 'link-55');">config</a></tt> <tt class="py-op">=</tt> <tt id="link-56" class="py-name" targets="Function Bio.Mindy.BaseDB.read_config()=Bio.Mindy.BaseDB-module.html#read_config"><a title="Bio.Mindy.BaseDB.read_config" class="py-name" href="#" onclick="return doclink('link-56', 'read_config', 'link-56');">read_config</a></tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-string">"config.dat"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-57" class="py-name"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-57', 'config', 'link-55');">config</a></tt><tt class="py-op">[</tt><tt class="py-string">"index"</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt class="py-name">index_type</tt><tt class="py-op">:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"FlatDB does not support %r index"</tt> <tt class="py-op">%</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">                            <tt class="py-op">(</tt><tt id="link-58" class="py-name"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-58', 'config', 'link-55');">config</a></tt><tt class="py-op">[</tt><tt class="py-string">"index"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_namespace</tt> <tt class="py-op">=</tt> <tt id="link-59" class="py-name"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-59', 'config', 'link-55');">config</a></tt><tt class="py-op">[</tt><tt class="py-string">"primary_namespace"</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 class="py-name">secondary_namespaces</tt> <tt class="py-op">=</tt> <tt id="link-60" class="py-name"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-60', 'config', 'link-55');">config</a></tt><tt class="py-op">[</tt><tt class="py-string">"secondary_namespaces"</tt><tt class="py-op">]</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">formatname</tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-61', 'config', 'link-55');">config</a></tt><tt class="py-op">[</tt><tt class="py-string">"format"</tt><tt class="py-op">]</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line"> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">        <tt class="py-name">filename_map</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">        <tt class="py-name">fileid_info</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt> <tt id="link-62" class="py-name" targets="Variable Martel.Time.v=Martel.Time-module.html#v"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-62', 'v', 'link-62');">v</a></tt> <tt class="py-keyword">in</tt> <tt id="link-63" class="py-name"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-63', 'config', 'link-55');">config</a></tt><tt class="py-op">.</tt><tt id="link-64" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-64', 'items', 'link-64');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">k</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"fileid_"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">            <tt class="py-name">fileid</tt> <tt class="py-op">=</tt> <tt class="py-name">k</tt><tt class="py-op">[</tt><tt class="py-number">7</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">            <tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt id="link-65" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-65', 'size', 'link-14');">size</a></tt> <tt class="py-op">=</tt> <tt id="link-66" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-66', 'v', 'link-62');">v</a></tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">            <tt class="py-name">fileid_info</tt><tt class="py-op">[</tt><tt class="py-name">fileid</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-67', 'v', 'link-62');">v</a></tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">            <tt class="py-name">filename_map</tt><tt class="py-op">[</tt><tt class="py-name">filename</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">fileid</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">getsize</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt id="link-68" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-68', 'size', 'link-14');">size</a></tt><tt class="py-op">:</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">                    <tt class="py-string">"File %s has changed size from %d to %d bytes!"</tt> <tt class="py-op">%</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">                    <tt class="py-op">(</tt><tt id="link-69" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-69', 'size', 'link-14');">size</a></tt><tt class="py-op">,</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">getsize</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename_map</tt> <tt class="py-op">=</tt> <tt class="py-name">filename_map</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fileid_info</tt> <tt class="py-op">=</tt> <tt class="py-name">fileid_info</tt> </tt>
</div><a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">         </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line"> </tt>
<a name="OpenDB.lookup"></a><div id="OpenDB.lookup-def"><a name="L106"></a><tt class="py-lineno">106</tt> <a class="py-toggle" href="#" id="OpenDB.lookup-toggle" onclick="return toggle('OpenDB.lookup');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB.OpenDB-class.html#lookup">lookup</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">kwargs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="OpenDB.lookup-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OpenDB.lookup-expanded"><a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">args</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">kwargs</tt><tt class="py-op">:</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot specify both args and kwargs"</tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Only one identifier handled"</tt><tt class="py-op">)</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">            <tt id="link-70" class="py-name" targets="Variable Bio.Std.namespace=Bio.Std-module.html#namespace,Variable Bio.biblio.namespace=Bio.biblio-module.html#namespace"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-70', 'namespace', 'link-70');">namespace</a></tt><tt class="py-op">,</tt> <tt id="link-71" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-71', 'name', 'link-32');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_namespace</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">         </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">kwargs</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"lookup takes a single key"</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">            <tt id="link-72" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-72', 'namespace', 'link-70');">namespace</a></tt><tt class="py-op">,</tt> <tt id="link-73" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-73', 'name', 'link-32');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">kwargs</tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-74', 'items', 'link-64');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</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 id="link-75" class="py-name"><a title="Bio.Std.namespace
Bio.biblio.namespace" class="py-name" href="#" onclick="return doclink('link-75', 'namespace', 'link-70');">namespace</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-76" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-76', 'name', 'link-32');">name</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line"> </tt>
<a name="OpenDB.__getitem__"></a><div id="OpenDB.__getitem__-def"><a name="L120"></a><tt class="py-lineno">120</tt> <a class="py-toggle" href="#" id="OpenDB.__getitem__-toggle" onclick="return toggle('OpenDB.__getitem__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB.OpenDB-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">namespace</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="OpenDB.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OpenDB.__getitem__-expanded"><a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">        <tt class="py-docstring">"""return the database table lookup for the given namespace"""</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-string">"must be implemented in the derived class"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line"> </tt>
<a name="OpenDB.keys"></a><div id="OpenDB.keys-def"><a name="L124"></a><tt class="py-lineno">124</tt> <a class="py-toggle" href="#" id="OpenDB.keys-toggle" onclick="return toggle('OpenDB.keys');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB.OpenDB-class.html#keys">keys</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="OpenDB.keys-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="OpenDB.keys-expanded"><a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">primary_namespace</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">secondary_namespaces</tt> </tt>
</div></div><a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line"> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line"><tt class="py-comment"># Write the configuration</tt> </tt>
<a name="write_config"></a><div id="write_config-def"><a name="L128"></a><tt class="py-lineno">128</tt> <a class="py-toggle" href="#" id="write_config-toggle" onclick="return toggle('write_config');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB-module.html#write_config">write_config</a><tt class="py-op">(</tt><tt class="py-param">config_filename</tt><tt class="py-op">,</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">                 <tt class="py-param">index_type</tt><tt class="py-op">,</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">                 <tt class="py-param">primary_namespace</tt><tt class="py-op">,</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">                 <tt class="py-param">secondary_namespaces</tt><tt class="py-op">,</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">                 <tt class="py-param">fileid_info</tt><tt class="py-op">,</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">                 <tt class="py-param">formatname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="write_config-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="write_config-expanded"><a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">    <tt class="py-name">configfile</tt> <tt class="py-op">=</tt> <tt id="link-77" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-77', 'open', 'link-77');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">config_filename</tt><tt class="py-op">,</tt> <tt class="py-string">"wb"</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">    <tt class="py-comment"># Write the header</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">configfile</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-78', 'write', 'link-78');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"index\t"</tt> <tt class="py-op">+</tt> <tt class="py-name">index_type</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line"> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">    <tt class="py-comment"># Write the namespace information</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">configfile</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-79', 'write', 'link-78');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"primary_namespace\t%s\n"</tt> <tt class="py-op">%</tt> <tt class="py-name">primary_namespace</tt><tt class="py-op">)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">    <tt id="link-80" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-80', 'keys', 'link-11');">keys</a></tt> <tt class="py-op">=</tt> <tt class="py-name">secondary_namespaces</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">    <tt id="link-81" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-81', 'keys', 'link-11');">keys</a></tt><tt class="py-op">.</tt><tt id="link-82" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-82', 'sort', 'link-82');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">    <tt class="py-name">configfile</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-83', 'write', 'link-78');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"secondary_namespaces\t"</tt><tt class="py-op">)</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">    <tt class="py-name">configfile</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-84', 'write', 'link-78');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-85" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-85', 'keys', 'link-11');">keys</a></tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line"> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">    <tt class="py-comment"># Format name</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">configfile</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-86', 'write', 'link-78');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"format\t"</tt> <tt class="py-op">+</tt> <tt class="py-name">formatname</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line"> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">    <tt class="py-comment"># Write the fileid table</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-87" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-87', 'items', 'link-64');">items</a></tt> <tt class="py-op">=</tt> <tt class="py-name">fileid_info</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-88', 'items', 'link-64');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">    <tt id="link-89" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-89', 'items', 'link-64');">items</a></tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-90', 'sort', 'link-82');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">fileid</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt id="link-91" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-91', 'size', 'link-14');">size</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt id="link-92" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-92', 'items', 'link-64');">items</a></tt><tt class="py-op">:</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">        <tt class="py-name">configfile</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-93', 'write', 'link-78');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"fileid_%s\t%s\t%s\n"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">                         <tt class="py-op">(</tt><tt class="py-name">fileid</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt id="link-94" class="py-name" targets="Function Bio.Mindy.BaseDB._int_str()=Bio.Mindy.BaseDB-module.html#_int_str"><a title="Bio.Mindy.BaseDB._int_str" class="py-name" href="#" onclick="return doclink('link-94', '_int_str', 'link-94');">_int_str</a></tt><tt class="py-op">(</tt><tt id="link-95" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size
Bio.Alphabet.Alphabet.size
Bio.Alphabet.Reduced.HPModel.size
Bio.Alphabet.Reduced.Murphy10.size
Bio.Alphabet.Reduced.Murphy15.size
Bio.Alphabet.Reduced.Murphy4.size
Bio.Alphabet.Reduced.Murphy8.size
Bio.Alphabet.Reduced.PC5.size
Bio.Alphabet.SingleLetterAlphabet.size
Bio.Alphabet.ThreeLetterProtein.size
Bio.GenBank._FeatureConsumer.size
Bio.GenBank._RecordConsumer.size
Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-95', 'size', 'link-14');">size</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line"> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">    <tt class="py-name">configfile</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-96', 'close', 'link-96');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line"> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line"> </tt>
<a name="read_config"></a><div id="read_config-def"><a name="L159"></a><tt class="py-lineno">159</tt> <a class="py-toggle" href="#" id="read_config-toggle" onclick="return toggle('read_config');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.BaseDB-module.html#read_config">read_config</a><tt class="py-op">(</tt><tt class="py-param">config_filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="read_config-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="read_config-expanded"><a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">    <tt id="link-97" class="py-name" targets="Variable Bio.EUtils.setup.d=Bio.EUtils.setup-module.html#d"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-97', 'd', 'link-97');">d</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-98" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-98', 'open', 'link-77');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">config_filename</tt><tt class="py-op">,</tt> <tt class="py-string">"rb"</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-99', 'read', 'link-99');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-100" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-100', 'split', 'link-100');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">        <tt class="py-name">words</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-101', 'split', 'link-100');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-keyword">not</tt> <tt id="link-102" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-102', 'd', 'link-97');">d</a></tt><tt class="py-op">.</tt><tt id="link-103" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-103', 'has_key', 'link-103');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">words</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-op">,</tt> \ </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">               <tt class="py-string">"Duplicate key %r in config file: old = %r, new = %r"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">               <tt class="py-op">(</tt><tt class="py-name">words</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-104" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-104', 'd', 'link-97');">d</a></tt><tt class="py-op">[</tt><tt class="py-name">words</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-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">words</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"index"</tt><tt class="py-op">,</tt> <tt class="py-string">"primary_namespace"</tt><tt class="py-op">,</tt> <tt class="py-string">"format"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">words</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">(</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">                    <tt class="py-string">"%s should only have one value, not %r"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">                    <tt class="py-op">(</tt><tt class="py-name">words</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">words</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 class="py-op">)</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">            <tt id="link-105" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-105', 'd', 'link-97');">d</a></tt><tt class="py-op">[</tt><tt class="py-name">words</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-op">=</tt> <tt class="py-name">words</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">             </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">words</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">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"fileid_"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">words</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">3</tt><tt class="py-op">:</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">(</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">                    <tt class="py-string">"%s should only have two values, not %r"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">                    <tt class="py-op">(</tt><tt class="py-name">words</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">words</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 class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">            <tt id="link-106" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-106', 'd', 'link-97');">d</a></tt><tt class="py-op">[</tt><tt class="py-name">words</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-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">words</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-name">long</tt><tt class="py-op">(</tt><tt class="py-name">words</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">         </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">words</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"secondary_namespaces"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">            <tt class="py-comment"># This can have 0 or more values</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt id="link-107" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-107', 'd', 'link-97');">d</a></tt><tt class="py-op">[</tt><tt class="py-name">words</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-op">=</tt> <tt class="py-name">words</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="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-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">            <tt class="py-comment"># Unknown word, save as-is</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt id="link-108" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-108', 'd', 'link-97');">d</a></tt><tt class="py-op">[</tt><tt class="py-name">words</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-op">=</tt> <tt class="py-name">words</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="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">     </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-109" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-109', 'd', 'link-97');">d</a></tt> </tt>
</div><a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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