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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.expressions-module.html">Package expressions</a> ::
<a href="Bio.expressions.swissprot-module.html">Package swissprot</a> ::
Module sprot40
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module sprot40</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.expressions.swissprot.sprot40-pysrc.html">source code</a></span></p>
<!-- ==================== VARIABLES ==================== -->
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<td align="left"><span class="table-header">Variables</span></td>
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<span class="summary-type"> </span>
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<a href="Bio.expressions.swissprot.sprot40-module.html#DT_created_exp" class="summary-name">DT_created_exp</a> = <code title="Martel.Str("DT ")+ Time.make_expression("%(DD)-%(Jan)-%(YYYY)")+ Mar\
tel.Re(" \(R[Ee][Ll]. (?P<release>\d\d), Created\)\R")">Martel.Str("DT ")+ Time.make_expression("%(<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.swissprot.sprot40-module.html#OX_start" class="summary-name">OX_start</a> = <code title="Martel.Str("OX NCBI_TaxID=")+ Martel.Rep1(Martel.Digits("ncbi_taxid"\
)+ Martel.Re("[,; ]+"))+ Martel.AnyEol()">Martel.Str("OX NCBI_TaxID=")+ Martel.Rep1(Martel.<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.swissprot.sprot40-module.html#OX_cont" class="summary-name">OX_cont</a> = <code title="Martel.Str("OX ")+ Martel.Rep1(Martel.Digits("ncbi_taxid")+ Martel.R\
e("[,; ]+"))+ Martel.AnyEol()">Martel.Str("OX ")+ Martel.Rep1(Martel.Digits("ncbi<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="OX_exp"></a><span class="summary-name">OX_exp</span> = <code title="OX_start+ Martel.Rep(OX_cont)">OX_start+ Martel.Rep(OX_cont)</code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.swissprot.sprot40-module.html#bib" class="summary-name">bib</a> = <code title="Martel.Word("bibliographic_database_name")+ Martel.Str("=")+ Martel.To\
Sep("bibliographic_identifier", ";")">Martel.Word("bibliographic_database_name")+ Martel.Str("<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.swissprot.sprot40-module.html#RX_exp" class="summary-name">RX_exp</a> = <code title="Martel.Str("RX ")+ bib+ Martel.Opt(Martel.Str(" ")+ bib)+ Martel.Any\
Eol()">Martel.Str("RX ")+ bib+ Martel.Opt(Martel.Str(" ")+<code class="variable-ellipsis">...</code></code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.swissprot.sprot40-module.html#SQ_exp" class="summary-name">SQ_exp</a> = <code title="Martel.Re("SQ SEQUENCE +(?P<sequence_length>\d+) AA;" " +(?P<molecul\
ar_weight>\d+) MW;" " +(?P<crc?type=64>\w+) CRC64;\R")">Martel.Re("SQ SEQUENCE +(?P<sequence_length>\d+) AA<code class="variable-ellipsis">...</code></code>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.swissprot.sprot40-module.html#replacements" class="summary-name">replacements</a> = <code title="[("DT_created", DT_created_exp), ("OX_block", OX_exp), ("RX", RX_exp),\
("SQ", SQ_exp),]">[("DT_created", DT_created_exp), ("OX_block", O<code class="variable-ellipsis">...</code></code>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="record"></a><span class="summary-name">record</span> = <code title="Martel.replace_groups(sprot38.record, replacements)">Martel.replace_groups(sprot38.record, replacements)</code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.swissprot.sprot40-module.html#format_expression" class="summary-name">format_expression</a> = <code title="Martel.replace_groups(sprot38.format_expression, replacements)">Martel.replace_groups(sprot38.format_expre<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="format"></a><span class="summary-name">format</span> = <code title="Martel.replace_groups(sprot38.format, replacements)">Martel.replace_groups(sprot38.format, replacements)</code>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.swissprot.sprot40-module.html#__warningregistry__" class="summary-name">__warningregistry__</a> = <code title="{('Bio.expressions was deprecated, as it does not work with recent ver\
sions of mxTextTools. If you want to continue to use this module, plea\
se get in contact with the Biopython developers at biopython-dev@biopy\
thon.org to avoid permanent removal of this module from Biopython',
<type 'exceptions.DeprecationWarning'>,
2): 1}"><code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Bio.expressions was deprecated, as it</code><code class="variable-ellipsis">...</code></code>
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<!-- ==================== VARIABLES DETAILS ==================== -->
<a name="section-VariablesDetails"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<td colspan="2" class="table-header">
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<td align="left"><span class="table-header">Variables Details</span></td>
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><span class="options">[<a href="#section-VariablesDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<a name="DT_created_exp"></a>
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<tr><td>
<h3 class="epydoc">DT_created_exp</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Str("DT ")+ Time.make_expression("%(DD)-%(Jan)-%(YYYY)")+ Mar<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
tel.Re(" \(R[Ee][Ll]. (?P<release>\d\d), Created\)\R")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="OX_start"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">OX_start</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Str("OX NCBI_TaxID=")+ Martel.Rep1(Martel.Digits("ncbi_taxid"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ Martel.Re("[,; ]+"))+ Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="OX_cont"></a>
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">OX_cont</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Str("OX ")+ Martel.Rep1(Martel.Digits("ncbi_taxid")+ Martel.R<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
e("[,; ]+"))+ Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="bib"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">bib</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Word("bibliographic_database_name")+ Martel.Str("=")+ Martel.To<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Sep("bibliographic_identifier", ";")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="RX_exp"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">RX_exp</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Str("RX ")+ bib+ Martel.Opt(Martel.Str(" ")+ bib)+ Martel.Any<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Eol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="SQ_exp"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">SQ_exp</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Re("SQ SEQUENCE +(?P<sequence_length>\d+) AA;" " +(?P<molecul<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ar_weight>\d+) MW;" " +(?P<crc?type=64>\w+) CRC64;\R")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="replacements"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">replacements</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
[("DT_created", DT_created_exp), ("OX_block", OX_exp), ("RX", RX_exp),<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
("SQ", SQ_exp),]
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="format_expression"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">format_expression</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.replace_groups(sprot38.format_expression, replacements)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="__warningregistry__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">__warningregistry__</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Bio.expressions was deprecated, as it does not work with recent ver</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">sions of mxTextTools. If you want to continue to use this module, plea</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">se get in contact with the Biopython developers at biopython-dev@biopy</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">thon.org to avoid permanent removal of this module from Biopython</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<type 'exceptions.DeprecationWarning'><code class="variable-op">,</code>
2<code class="variable-group">)</code><code class="variable-op">: </code>1<code class="variable-group">}</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
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