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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.dbdefs-module.html">Package dbdefs</a> ::
Module genbank
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module genbank</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.dbdefs.genbank-pysrc.html">source code</a></span></p>
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<span class="summary-type"> </span>
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<a href="Bio.dbdefs.genbank-module.html#proxy_error_expr" class="summary-name">proxy_error_expr</a> = <code title="has_expr(Alt(Str("500"), Str("502"))+ Str(" Proxy Error"))">has_expr(Alt(Str("500"), Str("502"))+ Str("<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a name="diagnostic_error_expr"></a><span class="summary-name">diagnostic_error_expr</span> = <code title="has_str("WWW Error 500 Diagnostic")">has_str("WWW Error 500 Diagnostic")</code>
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<span class="summary-type"> </span>
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<a name="error_expr"></a><span class="summary-name">error_expr</span> = <code title="Str("ERROR")">Str("ERROR")</code>
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<span class="summary-type"> </span>
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<a href="Bio.dbdefs.genbank-module.html#ncbi_failures" class="summary-name">ncbi_failures</a> = <code title="[(proxy_error_expr, "proxy error"), (diagnostic_error_expr, "diagnosti\
c error"), (error_expr, "ERROR"), (html_expr, "I got HTML and shouldn'\
t have"), (Str("Please try again later"), "Please try again later"), (\
Str("The sequence has been intentionally withdrawn"), "Sequence withdr\
awn"), (blank_expr, "No data returned")]">[(proxy_error_expr, "proxy error"), (diagnosti<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a href="Bio.dbdefs.genbank-module.html#nucleotide_genbank_eutils" class="summary-name">nucleotide_genbank_eutils</a> = <code title="EUtilsDB(name= "nucleotide-genbank-eutils", doc= "Retrieve nucleotide \
GenBank sequences from NCBI using EUtils", delay= 5.0, db= "nucleotide\
", rettype= "gb", failure_cases= ncbi_failures)">EUtilsDB(name= "nucleotide-genbank<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a href="Bio.dbdefs.genbank-module.html#genome_genbank_eutils" class="summary-name">genome_genbank_eutils</a> = <code title="EUtilsDB(name= "genome-genbank-eutils", doc= "Retrieve genome GenBank \
sequences from NCBI using EUtils", delay= 5.0, db= "genome", rettype= \
"gb", failure_cases= ncbi_failures)">EUtilsDB(name= "genome-genbank-eutils"<code class="variable-ellipsis">...</code></code>
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<a href="Bio.dbdefs.genbank-module.html#not_exist_expr" class="summary-name">not_exist_expr</a> = <code title="Str("ERROR")+ Re("[^d]*")+ Str("does not exist for gi")">Str("ERROR")+ Re("[^d]*")+ Str("does not exis<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a href="Bio.dbdefs.genbank-module.html#protein_genbank_eutils" class="summary-name">protein_genbank_eutils</a> = <code title="EUtilsDB(name= "protein-genbank-eutils", doc= "Retrieve protein GenPep\
t sequences from NCBI using EUtils", delay= 5.0, db= "protein", rettyp\
e= "gp", failure_cases= ncbi_failures+ [(not_exist_expr, "GI does not \
exist")])">EUtilsDB(name= "protein-genbank-eutil<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a href="Bio.dbdefs.genbank-module.html#gb_nucleotide" class="summary-name">gb_nucleotide</a> = <code title="DBGroup(name= "genbank-nucleotide", behavior= "serial")">DBGroup(name= "genbank-nucleotide", behavior= <code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a name="gb_protein"></a><span class="summary-name">gb_protein</span> = <code title="DBGroup(name= "genbank-protein", behavior= "serial")">DBGroup(name= "genbank-protein", behavior= "serial")</code>
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<span class="summary-type"> </span>
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<a name="gb_genome"></a><span class="summary-name">gb_genome</span> = <code title="DBGroup(name= "genbank-genome", behavior= "serial")">DBGroup(name= "genbank-genome", behavior= "serial")</code>
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<h3 class="epydoc">proxy_error_expr</h3>
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<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
has_expr(Alt(Str("500"), Str("502"))+ Str(" Proxy Error"))
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<a name="ncbi_failures"></a>
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<h3 class="epydoc">ncbi_failures</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
[(proxy_error_expr, "proxy error"), (diagnostic_error_expr, "diagnosti<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
c error"), (error_expr, "ERROR"), (html_expr, "I got HTML and shouldn'<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
t have"), (Str("Please try again later"), "Please try again later"), (<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Str("The sequence has been intentionally withdrawn"), "Sequence withdr<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
awn"), (blank_expr, "No data returned")]
</pre></td></tr></table>
</dd>
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<a name="nucleotide_genbank_eutils"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc">nucleotide_genbank_eutils</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
EUtilsDB(name= "nucleotide-genbank-eutils", doc= "Retrieve nucleotide <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
GenBank sequences from NCBI using EUtils", delay= 5.0, db= "nucleotide<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
", rettype= "gb", failure_cases= ncbi_failures)
</pre></td></tr></table>
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<a name="genome_genbank_eutils"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc">genome_genbank_eutils</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
EUtilsDB(name= "genome-genbank-eutils", doc= "Retrieve genome GenBank <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
sequences from NCBI using EUtils", delay= 5.0, db= "genome", rettype= <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"gb", failure_cases= ncbi_failures)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
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<a name="not_exist_expr"></a>
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<h3 class="epydoc">not_exist_expr</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str("ERROR")+ Re("[^d]*")+ Str("does not exist for gi")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
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<a name="protein_genbank_eutils"></a>
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<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">protein_genbank_eutils</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
EUtilsDB(name= "protein-genbank-eutils", doc= "Retrieve protein GenPep<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
t sequences from NCBI using EUtils", delay= 5.0, db= "protein", rettyp<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
e= "gp", failure_cases= ncbi_failures+ [(not_exist_expr, "GI does not <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
exist")])
</pre></td></tr></table>
</dd>
</dl>
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<a name="gb_nucleotide"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc">gb_nucleotide</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
DBGroup(name= "genbank-nucleotide", behavior= "serial")
</pre></td></tr></table>
</dd>
</dl>
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