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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.expressions-module.html">Package expressions</a> ::
Module transfac
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module transfac</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.expressions.transfac-pysrc.html">source code</a></span></p>
<p>A Martel format to parse the output from transfac.</p>
<p>Formats: format Format for a whole file.</p>
<!-- ==================== FUNCTIONS ==================== -->
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<td align="left"><span class="table-header">Functions</span></td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="SS"></a><span class="summary-sig-name">SS</span>(<span class="summary-sig-arg">exp</span>)</span></td>
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<span class="codelink"><a href="Bio.expressions.transfac-pysrc.html#SS">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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class="privatelink" onclick="toggle_private();"
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="blank_line"></a><span class="summary-name">blank_line</span> = <code title="Opt(Spaces())+ AnyEol()">Opt(Spaces())+ AnyEol()</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.transfac-module.html#MATRIX_LINE" class="summary-name">MATRIX_LINE</a> = <code title="Str("Search for sites by WeightMatrix library:")+ Spaces()+ UntilEol("\
matrix_file")+ AnyEol()">Str("Search for sites by WeightMatrix library:")<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.transfac-module.html#SEQUENCE_LINE" class="summary-name">SEQUENCE_LINE</a> = <code title="Str("Sequence file:")+ Spaces()+ UntilEol("sequence_file")+ AnyEol()">Str("Sequence file:")+ Spaces()+ UntilEol("seq<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.transfac-module.html#PROFILE_LINE" class="summary-name">PROFILE_LINE</a> = <code title="Str("Site selection profile:")+ Spaces()+ UntilSep("profile_file", sep\
= " ")+ Spaces()+ UntilEol("profile_description")+ AnyEol()">Str("Site selection profile:")+ Spaces()+ Until<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.transfac-module.html#TITLE_LINE" class="summary-name">TITLE_LINE</a> = <code title="Str("Inspecting sequence ID")+ Spaces()+ UntilSep("entryname", sep= " \
")+ Spaces()+ UntilSep("dataclass", sep= ";")+ Str(";")+ Spaces()+ Unt\
ilSep("molecule", sep= ";")+ Str(";")+ Spaces()+ UntilSep("division", \
sep= ";")+ Str(";")+ Spaces()+ UntilSep("sequencelength", sep= " ")+ S\
paces()+ Str("BP")+ UntilEol()+ AnyEol()">Str("Inspecting sequence ID")+ Spaces()+ UntilSep<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.transfac-module.html#DATA_LINE" class="summary-name">DATA_LINE</a> = <code title="SS(UntilSep("matrix_identifier", sep= " |"))+ Str("|")+ SS(UntilSep("p\
osition", sep= " "))+ SS(Str("(")+ Group("strand", Any("+-"))+ Str(")"\
))+ Str("|")+ SS(Float("core_match"))+ Str("|")+ SS(Float("matrix_matc\
h"))+ Str("|")+ Opt(Spaces())+ UntilEol("sequence")+ AnyEol()">SS(UntilSep("matrix_identifier", sep= " |"))+ Str(<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.transfac-module.html#SEQUENCES_LENGTH_LINE" class="summary-name">SEQUENCES_LENGTH_LINE</a> = <code title="Spaces()+ Str("Total sequences length=")+ Integer("sequences_length")+\
AnyEol()">Spaces()+ Str("Total sequences length=<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.transfac-module.html#FOUND_SITES_LINE" class="summary-name">FOUND_SITES_LINE</a> = <code title="Spaces()+ Str("Total number of found sites=")+ Integer("found_sites")+\
AnyEol()">Spaces()+ Str("Total number of found sites=<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.transfac-module.html#SITE_FREQUENCY_LINE" class="summary-name">SITE_FREQUENCY_LINE</a> = <code title="Spaces()+ Str("Frequency of sites per nucleotide=")+ Float("sites_per_\
nucleotide")+ AnyEol()">Spaces()+ Str("Frequency of sites per nu<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.transfac-module.html#format" class="summary-name">format</a> = <code title="MATRIX_LINE+ SEQUENCE_LINE+ PROFILE_LINE+ blank_line+ TITLE_LINE+ blan\
k_line+ Rep(DATA_LINE)+ blank_line+ SEQUENCES_LENGTH_LINE+ blank_line+\
FOUND_SITES_LINE+ blank_line+ SITE_FREQUENCY_LINE">MATRIX_LINE+ SEQUENCE_LINE+ PROFILE_LINE+ blank_line+<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.transfac-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>
</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="MATRIX_LINE"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">MATRIX_LINE</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str("Search for sites by WeightMatrix library:")+ Spaces()+ UntilEol("<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
matrix_file")+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="SEQUENCE_LINE"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">SEQUENCE_LINE</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str("Sequence file:")+ Spaces()+ UntilEol("sequence_file")+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="PROFILE_LINE"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">PROFILE_LINE</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str("Site selection profile:")+ Spaces()+ UntilSep("profile_file", sep<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
= " ")+ Spaces()+ UntilEol("profile_description")+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="TITLE_LINE"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">TITLE_LINE</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str("Inspecting sequence ID")+ Spaces()+ UntilSep("entryname", sep= " <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
")+ Spaces()+ UntilSep("dataclass", sep= ";")+ Str(";")+ Spaces()+ Unt<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ilSep("molecule", sep= ";")+ Str(";")+ Spaces()+ UntilSep("division", <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
sep= ";")+ Str(";")+ Spaces()+ UntilSep("sequencelength", sep= " ")+ S<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
paces()+ Str("BP")+ UntilEol()+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="DATA_LINE"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">DATA_LINE</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
SS(UntilSep("matrix_identifier", sep= " |"))+ Str("|")+ SS(UntilSep("p<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
osition", sep= " "))+ SS(Str("(")+ Group("strand", Any("+-"))+ Str(")"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
))+ Str("|")+ SS(Float("core_match"))+ Str("|")+ SS(Float("matrix_matc<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
h"))+ Str("|")+ Opt(Spaces())+ UntilEol("sequence")+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="SEQUENCES_LENGTH_LINE"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">SEQUENCES_LENGTH_LINE</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Spaces()+ Str("Total sequences length=")+ Integer("sequences_length")+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="FOUND_SITES_LINE"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">FOUND_SITES_LINE</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Spaces()+ Str("Total number of found sites=")+ Integer("found_sites")+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="SITE_FREQUENCY_LINE"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">SITE_FREQUENCY_LINE</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Spaces()+ Str("Frequency of sites per nucleotide=")+ Float("sites_per_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
nucleotide")+ AnyEol()
</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">
MATRIX_LINE+ SEQUENCE_LINE+ PROFILE_LINE+ blank_line+ TITLE_LINE+ blan<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
k_line+ Rep(DATA_LINE)+ blank_line+ SEQUENCES_LENGTH_LINE+ blank_line+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
FOUND_SITES_LINE+ blank_line+ SITE_FREQUENCY_LINE
</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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