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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.LocusLink-module.html">Package LocusLink</a> ::
Module locus_format
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module locus_format</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.LocusLink.locus_format-pysrc.html">source code</a></span></p>
<pre class="literalblock">
Martel based parser to read LocusLink flat files.
This is a huge regular expression for LocusLink,
built using the 'regular expressions on steroids' capabilities of
Martel.
A description of the format can be found in the 'ligand.doc' file
from the Ligand distribution, available from:
http://www.ncbi.nih.gov/LocusLink
</pre>
<!-- ==================== FUNCTIONS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="define_locus_line"></a><span class="summary-sig-name">define_locus_line</span>(<span class="summary-sig-arg">entry_tag</span>)</span></td>
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<span class="codelink"><a href="Bio.LocusLink.locus_format-pysrc.html#define_locus_line">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="define_locus_group"></a><span class="summary-sig-name">define_locus_group</span>(<span class="summary-sig-arg">entry_name</span>,
<span class="summary-sig-arg">entry_tag</span>)</span></td>
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<span class="codelink"><a href="Bio.LocusLink.locus_format-pysrc.html#define_locus_group">source code</a></span>
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<!-- ==================== VARIABLES ==================== -->
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<a name="INDENT"></a><span class="summary-name">INDENT</span> = <code title="12">12</code>
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<span class="summary-type"> </span>
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<a name="blank_spaces"></a><span class="summary-name">blank_spaces</span> = <code title="Rep(Str1(" "))">Rep(Str1(" "))</code>
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<span class="summary-type"> </span>
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<a name="point"></a><span class="summary-name">point</span> = <code title="Str1(".")">Str1(".")</code>
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<span class="summary-type"> </span>
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<a name="white_space"></a><span class="summary-name">white_space</span> = <code title="Rep(Any(" "))">Rep(Any(" "))</code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.LocusLink.locus_format-module.html#locus_keys" class="summary-name">locus_keys</a> = <code title="['LOCUSID',
'LOCUS_CONFIRMED',
'LOCUS_TYPE',
'ORGANISM',
'STATUS',
'NM',
'NP',
'CDD',
..."><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">LOCUSID</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">LOCUS_CONFIRMED</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">LOCUS_TYPE</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ORG</code><code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="accnum_block_keys"></a><span class="summary-name">accnum_block_keys</span> = <code title="['ACCNUM', 'TYPE', 'PROT']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">ACCNUM</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">TYPE</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">PROT</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="phenotype"></a><span class="summary-name">phenotype</span> = <code title="Str1('PHENOTYPE')">Str1('PHENOTYPE')</code>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="db"></a><span class="summary-name">db</span> = <code title="Str1('DB')">Str1('DB')</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="accnum_block_key"></a><span class="summary-name">accnum_block_key</span> = <code title="Str(* accnum_block_keys)">Str(* accnum_block_keys)</code>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="valid_locus_key"></a><span class="summary-name">valid_locus_key</span> = <code title="Str(* locus_keys)">Str(* locus_keys)</code>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.LocusLink.locus_format-module.html#accnum_block" class="summary-name">accnum_block</a> = <code title="Group('accnum_block', define_locus_line('ACCNUM')+ define_locus_line('\
TYPE')+ Opt(define_locus_line('PROT')))">Group('accnum_block', define_locus_line('ACCNUM<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.LocusLink.locus_format-module.html#phenotype_block" class="summary-name">phenotype_block</a> = <code title="Group('phenotype_block', define_locus_line('PHENOTYPE')+ Opt(define_lo\
cus_line('PHENOTYPE_ID')))">Group('phenotype_block', define_locus_line('<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.LocusLink.locus_format-module.html#db_block" class="summary-name">db_block</a> = <code title="Group('db_block', define_locus_line('DB_DESCR')+ define_locus_line('DB\
_LINK'))">Group('db_block', define_locus_line('DB_DESCR')+ de<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="begin_record_line"></a><span class="summary-name">begin_record_line</span> = <code title="Str1('>>')+ ToEol()">Str1('>>')+ ToEol()</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.LocusLink.locus_format-module.html#locus_line" class="summary-name">locus_line</a> = <code title="Group('locus_line', white_space+ AssertNot(accnum_block_key)+ AssertNo\
t(phenotype)+ AssertNot(db)+ Word()+ white_space+ Str1(':')+ ToEol())">Group('locus_line', white_space+ AssertNot(accnum<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.LocusLink.locus_format-module.html#locus_record" class="summary-name">locus_record</a> = <code title="begin_record_line+ Rep(Alt(locus_line, accnum_block, phenotype_block, \
db_block))">begin_record_line+ Rep(Alt(locus_line, accnum_b<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.LocusLink.locus_format-module.html#__warningregistry__" class="summary-name">__warningregistry__</a> = <code title="{('Bio.LocusLink was deprecated, as NCBI\'s LocusLink was superceded b\
y Entrez Gene. If you still need this module, please get in touch with\
the Biopython developers (biopython-dev@biopython.org) to avoid perma\
nent removal of this module',
<type 'exceptions.DeprecationWarning'>,
34): 1}"><code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Bio.LocusLink was deprecated, as NCBI</code><code class="variable-ellipsis">...</code></code>
</td>
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<!-- ==================== VARIABLES DETAILS ==================== -->
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<a name="locus_keys"></a>
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">locus_keys</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-quote">'</code><code class="variable-string">LOCUSID</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">LOCUS_CONFIRMED</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">LOCUS_TYPE</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ORGANISM</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">STATUS</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">NM</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">NP</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">CDD</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-ellipsis">...</code>
</pre></td></tr></table>
</dd>
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<a name="accnum_block"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">accnum_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group('accnum_block', define_locus_line('ACCNUM')+ define_locus_line('<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
TYPE')+ Opt(define_locus_line('PROT')))
</pre></td></tr></table>
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<a name="phenotype_block"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">phenotype_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group('phenotype_block', define_locus_line('PHENOTYPE')+ Opt(define_lo<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
cus_line('PHENOTYPE_ID')))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
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<a name="db_block"></a>
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">db_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group('db_block', define_locus_line('DB_DESCR')+ define_locus_line('DB<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_LINK'))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="locus_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">locus_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group('locus_line', white_space+ AssertNot(accnum_block_key)+ AssertNo<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
t(phenotype)+ AssertNot(db)+ Word()+ white_space+ Str1(':')+ ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="locus_record"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">locus_record</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
begin_record_line+ Rep(Alt(locus_line, accnum_block, phenotype_block, <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
db_block))
</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.LocusLink was deprecated, as NCBI\'s LocusLink was superceded b</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">y Entrez Gene. If you still need this module, please get in touch with</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string"> the Biopython developers (biopython-dev@biopython.org) to avoid perma</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">nent removal of this module</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<type 'exceptions.DeprecationWarning'><code class="variable-op">,</code>
34<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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