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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 speclist
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module speclist</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.expressions.swissprot.speclist-pysrc.html">source code</a></span></p>
<p>Parser for the SPECLIST.TXT file in SWISS-PROT.</p>
<p>You probably want to use the variables 'record' (for a single record)
and 'format' (for a set of records).</p>
<!-- ==================== FUNCTIONS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="SkipLinesToNoEOL"></a><span class="summary-sig-name">SkipLinesToNoEOL</span>(<span class="summary-sig-arg">expr</span>)</span></td>
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<span class="codelink"><a href="Bio.expressions.swissprot.speclist-pysrc.html#SkipLinesToNoEOL">source code</a></span>
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<!-- ==================== VARIABLES ==================== -->
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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.speclist-module.html#DESCRIPTION" class="summary-name">DESCRIPTION</a> = <code title="Str("Description:")+ Spaces()+ UntilEol("description")+ AnyEol()">Str("Description:")+ Spaces()+ UntilEol("descrip<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="NAME"></a><span class="summary-name">NAME</span> = <code title="Str("Name:")+ Spaces()+ UntilEol("name")+ AnyEol()">Str("Name:")+ Spaces()+ UntilEol("name")+ AnyEol()</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.speclist-module.html#RELEASE" class="summary-name">RELEASE</a> = <code title="Str("Release:")+ Spaces()+ UntilEol("release")+ AnyEol()">Str("Release:")+ Spaces()+ UntilEol("release")+ AnyE<code class="variable-ellipsis">...</code></code>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.swissprot.speclist-module.html#TOTAL_CODES" class="summary-name">TOTAL_CODES</a> = <code title="Str("Total number of organism identification codes currently defined:"\
)+ Spaces()+ Integer("num_organism_codes")+ Str(".")+ AnyEol()">Str("Total number of organism identification cod<code class="variable-ellipsis">...</code></code>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.swissprot.speclist-module.html#TABLE_HEADER" class="summary-name">TABLE_HEADER</a> = <code title="Group("table_header", Str("Code")+ Spaces()+ Str("Taxon")+ Spaces()+ S\
tr("N=Official name")+ ToEol()+ Spaces()+ Str("Node")+ Spaces()+ Str("\
C=Common name")+ ToEol()+ Spaces()+ Str("S=Synonym")+ ToEol()+ Rep1(An\
y(" _"))+ AnyEol())">Group("table_header", Str("Code")+ Spaces()+ St<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="_dash_line"></a><span class="summary-name">_dash_line</span> = <code title="Rep1(Str("-"))+ AnyEol()">Rep1(Str("-"))+ AnyEol()</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.speclist-module.html#COPYRIGHT" class="summary-name">COPYRIGHT</a> = <code title="Group("copyright", _dash_line+ Str("SWISS-PROT is copyright.")+ ToEol(\
)+ SkipLinesToNoEOL(_dash_line)+ Rep(AnyEol()))">Group("copyright", _dash_line+ Str("SWISS-PROT is <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.speclist-module.html#_code_line" class="summary-name" onclick="show_private();">_code_line</a> = <code title="Group("code", Re(r"[A-Z0-9]{1,5}"))+ Spaces()+ Group("kingdom", Any("A\
BEV"))+ Spaces()+ Group("taxon_node", Digits())+ Str(":")+ Spaces()+ S\
tr("N=")+ Group("official_name", UntilEol())+ AnyEol()">Group("code", Re(r"[A-Z0-9]{1,5}"))+ Spaces()+ Gr<code class="variable-ellipsis">...</code></code>
</td>
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<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.swissprot.speclist-module.html#_common_line" class="summary-name" onclick="show_private();">_common_line</a> = <code title="Spaces()+ Str("C=")+ Group("common_name", UntilEol())+ AnyEol()">Spaces()+ Str("C=")+ Group("common_name", Until<code class="variable-ellipsis">...</code></code>
</td>
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<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.swissprot.speclist-module.html#_synonym_line" class="summary-name" onclick="show_private();">_synonym_line</a> = <code title="Spaces()+ Str("S=")+ Group("synonym", UntilEol())+ AnyEol()">Spaces()+ Str("S=")+ Group("synonym", UntilEol<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 href="Bio.expressions.swissprot.speclist-module.html#record" class="summary-name">record</a> = <code title="Group("record", _code_line+ Rep(_common_line)+ Rep(_synonym_line))">Group("record", _code_line+ Rep(_common_line)+ Rep(_s<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.speclist-module.html#format" class="summary-name">format</a> = <code title="Group("format", SkipLinesToNoEOL(DESCRIPTION)+ NAME+ RELEASE+ SkipLine\
sToNoEOL(TOTAL_CODES)+ SkipLinesToNoEOL(TABLE_HEADER)+ Rep1(record)+ A\
nyEol()+ COPYRIGHT)">Group("format", SkipLinesToNoEOL(DESCRIPTION)+ NAME+ <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.speclist-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'>,
9): 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>
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<!-- ==================== 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="DESCRIPTION"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">DESCRIPTION</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str("Description:")+ Spaces()+ UntilEol("description")+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="RELEASE"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">RELEASE</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str("Release:")+ Spaces()+ UntilEol("release")+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="TOTAL_CODES"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">TOTAL_CODES</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str("Total number of organism identification codes currently defined:"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ Spaces()+ Integer("num_organism_codes")+ Str(".")+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="TABLE_HEADER"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">TABLE_HEADER</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("table_header", Str("Code")+ Spaces()+ Str("Taxon")+ Spaces()+ S<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
tr("N=Official name")+ ToEol()+ Spaces()+ Str("Node")+ Spaces()+ Str("<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
C=Common name")+ ToEol()+ Spaces()+ Str("S=Synonym")+ ToEol()+ Rep1(An<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
y(" _"))+ AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="COPYRIGHT"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">COPYRIGHT</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("copyright", _dash_line+ Str("SWISS-PROT is copyright.")+ ToEol(<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ SkipLinesToNoEOL(_dash_line)+ Rep(AnyEol()))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="_code_line"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">_code_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("code", Re(r"[A-Z0-9]{1,5}"))+ Spaces()+ Group("kingdom", Any("A<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
BEV"))+ Spaces()+ Group("taxon_node", Digits())+ Str(":")+ Spaces()+ S<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
tr("N=")+ Group("official_name", UntilEol())+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="_common_line"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">_common_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Spaces()+ Str("C=")+ Group("common_name", UntilEol())+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="_synonym_line"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">_synonym_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Spaces()+ Str("S=")+ Group("synonym", UntilEol())+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="record"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">record</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("record", _code_line+ Rep(_common_line)+ Rep(_synonym_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="format"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">format</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("format", SkipLinesToNoEOL(DESCRIPTION)+ NAME+ RELEASE+ SkipLine<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
sToNoEOL(TOTAL_CODES)+ SkipLinesToNoEOL(TABLE_HEADER)+ Rep1(record)+ A<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
nyEol()+ COPYRIGHT)
</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>
9<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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