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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 ipi
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module ipi</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.expressions.swissprot.ipi-pysrc.html">source code</a></span></p>
<p>Expression for IPI format.</p>
<p>IPI is nearly swissprot, but contains some differents which makes the
Swissprot parsers choke.</p>
<!-- ==================== VARIABLES ==================== -->
<a name="section-Variables"></a>
<table class="summary" border="1" cellpadding="3"
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<td align="left"><span class="table-header">Variables</span></td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.swissprot.ipi-module.html#ID_exp" class="summary-name">ID_exp</a> = <code title="Martel.Group("ID", Martel.Str("ID ")+ Std.dbid(Martel.Group("entry_n\
ame", Martel.Re("[\w.]+")), {"type": "primary", "dbname": "sp"})+ Mart\
el.Spaces()+ Martel.Word("data_class_table")+ Martel.Str(";")+ Martel.\
Spaces()+ Martel.Word("molecule_type")+ Martel.Str(";")+ Martel.Spaces\
()+ Martel.Digits("sequence_length")+ Martel.Str(" AA.")+ Martel.AnyEo\
l())">Martel.Group("ID", Martel.Str("ID ")+ Std.dbid(Mart<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 href="Bio.expressions.swissprot.ipi-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.Str(" (IPI Human rel. ")+ Martel.Float("release")+ Martel.Str(", C\
reated)")+ Martel.AnyEol()">Martel.Str("DT ")+ Time.make_expression("%(<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.ipi-module.html#DT_seq_update_exp" class="summary-name">DT_seq_update_exp</a> = <code title="Martel.Str("DT ")+ Time.make_expression("%(DD)-%(Jan)-%(YYYY)")+ Mar\
tel.Str(" (IPI Human rel. ")+ Martel.Float("release")+ Martel.Str(", L\
ast sequence update)")+ Martel.AnyEol()">Martel.Str("DT ")+ Time.make_expression(<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.swissprot.ipi-module.html#DT_ann_update_exp" class="summary-name">DT_ann_update_exp</a> = <code title="Martel.Str("DT ")+ Time.make_expression("%(DD)-%(Jan)-%(YYYY)")+ Mar\
tel.Str(" (IPI Human rel. ")+ Martel.Float("release")+ Martel.Str(", L\
ast annotation update)")+ Martel.AnyEol()">Martel.Str("DT ")+ Time.make_expression(<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 href="Bio.expressions.swissprot.ipi-module.html#replacements" class="summary-name">replacements</a> = <code title="[("ID", ID_exp), ("DT_created", DT_created_exp), ("DT_seq_update", DT_\
seq_update_exp), ("DT_ann_update", Martel.Opt(DT_ann_update_exp))]">[("ID", ID_exp), ("DT_created", DT_created_exp)<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<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(sprot40.record, replacements)">Martel.replace_groups(sprot40.record, 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.ipi-module.html#format_expression" class="summary-name">format_expression</a> = <code title="Martel.replace_groups(sprot40.format_expression, replacements)">Martel.replace_groups(sprot40.format_expre<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<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(sprot40.format, replacements)">Martel.replace_groups(sprot40.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.ipi-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'>,
8): 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>
</td>
</tr>
</table>
<!-- ==================== VARIABLES DETAILS ==================== -->
<a name="section-VariablesDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Variables Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-VariablesDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<a name="ID_exp"></a>
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<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">ID_exp</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("ID", Martel.Str("ID ")+ Std.dbid(Martel.Group("entry_n<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ame", Martel.Re("[\w.]+")), {"type": "primary", "dbname": "sp"})+ Mart<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
el.Spaces()+ Martel.Word("data_class_table")+ Martel.Str(";")+ Martel.<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Spaces()+ Martel.Word("molecule_type")+ Martel.Str(";")+ Martel.Spaces<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
()+ Martel.Digits("sequence_length")+ Martel.Str(" AA.")+ Martel.AnyEo<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
l())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="DT_created_exp"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<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.Str(" (IPI Human rel. ")+ Martel.Float("release")+ Martel.Str(", C<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
reated)")+ Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="DT_seq_update_exp"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">DT_seq_update_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.Str(" (IPI Human rel. ")+ Martel.Float("release")+ Martel.Str(", L<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ast sequence update)")+ Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="DT_ann_update_exp"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">DT_ann_update_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.Str(" (IPI Human rel. ")+ Martel.Float("release")+ Martel.Str(", L<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ast annotation update)")+ Martel.AnyEol()
</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">
[("ID", ID_exp), ("DT_created", DT_created_exp), ("DT_seq_update", DT_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
seq_update_exp), ("DT_ann_update", Martel.Opt(DT_ann_update_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(sprot40.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>
8<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>
</div>
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