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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.expressions-module.html">Package expressions</a> ::
Module hmmpfam
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module hmmpfam</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.expressions.hmmpfam-pysrc.html">source code</a></span></p>
<p>Martel expression for the hmmpfam database search program in
hmmer.</p>
<p>This has been tested with version 2.2g. I should also make it work
with 2.1.1 output.</p>
<p>XXX This isn't completely finished and doesn't do everything quite
right. The main two problems being that it isn't well tested for a wide
variety of outputs and that the family line is not parsed into it's
respective parts (see multitude of comments on this below).</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>
</td><td class="summary">
<a href="Bio.expressions.hmmpfam-module.html#program_description" class="summary-name">program_description</a> = <code title="Std.application_name(Str("hmmpfam"))+ ToEol()">Std.application_name(Str("hmmpfam"))+ To<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.hmmpfam-module.html#program_version" class="summary-name">program_version</a> = <code title="Str("HMMER ")+ Std.application_version(Re(r"\d\.\d\w") | Re(r"\d\.\d\.\
\d"))+ ToEol()">Str("HMMER ")+ Std.application_version(Re(r"<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="copyright"></a><span class="summary-name">copyright</span> = <code title="ToEol()+ ToEol()">ToEol()+ ToEol()</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.hmmpfam-module.html#files" class="summary-name">files</a> = <code title="ToEol()+ Str("HMM file:")+ Spaces()+ Std.database_name(UntilEol())+ An\
yEol()+ Str("Sequence file:")+ Spaces()+ Group("inputfile_name", Until\
Eol())+ AnyEol()+ ToEol()">ToEol()+ Str("HMM file:")+ Spaces()+ Std.database_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.hmmpfam-module.html#header" class="summary-name">header</a> = <code title="Std.search_header(program_description+ program_version+ copyright+ fil\
es)">Std.search_header(program_description+ program_versio<code class="variable-ellipsis">...</code></code>
</td>
</tr>
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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.hmmpfam-module.html#sequence_info" class="summary-name">sequence_info</a> = <code title="ToEol()+ Str("Query sequence:")+ Spaces()+ Group("query_name", UntilEo\
l())+ AnyEol()+ Str("Accession:")+ Spaces()+ Group("query_accession", \
UntilEol())+ AnyEol()+ Str("Description:")+ Spaces()+ Std.query_descri\
ption(UntilEol())+ AnyEol()">ToEol()+ Str("Query sequence:")+ Spaces()+ Gro<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="model_name"></a><span class="summary-name">model_name</span> = <code title="Re(r"[\w-]+")">Re(r"[\w-]+")</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.hmmpfam-module.html#family_header" class="summary-name">family_header</a> = <code title="ToEol()+ Str("Scores")+ ToEol()+ Str("Model")+ ToEol()+ Str("-----")+ \
ToEol()">ToEol()+ Str("Scores")+ ToEol()+ Str("Model")+<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.hmmpfam-module.html#no_hit_line" class="summary-name">no_hit_line</a> = <code title="Spaces()+ Str("[no hits above thresholds]")+ AnyEol()">Spaces()+ Str("[no hits above thresholds]")+ Any<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.hmmpfam-module.html#family_hit_line" class="summary-name">family_hit_line</a> = <code title="Group("family_model", model_name)+ Spaces()+ ToEol("family_information\
")">Group("family_model", model_name)+ Spaces()+<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.hmmpfam-module.html#domain_header" class="summary-name">domain_header</a> = <code title="ToEol()+ Str("Parsed for domains:")+ AnyEol()+ Str("Model")+ ToEol()+ \
Str("-----")+ ToEol()">ToEol()+ Str("Parsed for domains:")+ AnyEol()+<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="symbol_forward"></a><span class="summary-name">symbol_forward</span> = <code title="Str(".") | Str("[")">Str(".") | Str("[")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="symbol_reverse"></a><span class="summary-name">symbol_reverse</span> = <code title="Str(".") | Str("]")">Str(".") | Str("]")</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="match_symbols"></a><span class="summary-name">match_symbols</span> = <code title="symbol_forward+ symbol_reverse">symbol_forward+ symbol_reverse</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.hmmpfam-module.html#domain_hit_line" class="summary-name">domain_hit_line</a> = <code title="Group("domain_model", model_name)+ Spaces()+ Group("domain_domain", In\
teger()+ Str("/")+ Integer())+ Spaces()+ Integer("domain_seq-f")+ Spac\
es()+ Integer("domain_seq-r")+ Spaces()+ Group("domain_seq_symbols", m\
atch_symbols)+ Spaces()+ Integer("domain_hmm-f")+ Spaces()+ Integer("d\
omain_hmm-t")+ Spaces()+ Group("domain_hmm_symbols", match_symbols)+ S\
paces()+ Float("domain_score")+ Spaces()+ Float("domain_evalue")+ AnyE\
ol()">Group("domain_model", model_name)+ Spaces()+<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.hmmpfam-module.html#alignment_header" class="summary-name">alignment_header</a> = <code title="ToEol()+ Str("Alignments of top-scoring domains:")+ AnyEol()">ToEol()+ Str("Alignments of top-scoring dom<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.hmmpfam-module.html#domain_align_header" class="summary-name">domain_align_header</a> = <code title="Group("dalign_name", model_name)+ Str(": domain ")+ Integer("dalign_of\
_domain")+ Str(" of ")+ Integer("dalign_total_domain")+ Str(", from ")\
+ Integer("dalign_domain_start")+ Str(" to ")+ Integer("dalign_domain_\
end")+ Str(": score ")+ Float("dalign_score")+ Str(", E = ")+ Float("d\
align_evalue")+ AnyEol()">Group("dalign_name", model_name)+ Str(":<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="rf_line"></a><span class="summary-name">rf_line</span> = <code title="Spaces()+ Str("RF ")+ ToEol()">Spaces()+ Str("RF ")+ ToEol()</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.hmmpfam-module.html#domain_align_top" class="summary-name">domain_align_top</a> = <code title="Spaces()+ UntilEol("dalign_match_top")+ AnyEol()">Spaces()+ UntilEol("dalign_match_top")+ Any<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.hmmpfam-module.html#domain_align_middle" class="summary-name">domain_align_middle</a> = <code title="Spaces()+ UntilEol("dalign_match_middle")+ AnyEol()">Spaces()+ UntilEol("dalign_match_middle"<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.hmmpfam-module.html#domain_align_bottom" class="summary-name">domain_align_bottom</a> = <code title="Spaces()+ ToSep("dalign_query_name", " ")+ Spaces()+ Alt(Integer("dali\
gn_query_start")+ Spaces()+ Group("dalign_match_bottom", Re("[\w\-]+")\
)+ Spaces()+ Integer("dalign_query_end")+ Spaces()+ AnyEol(), Str("- "\
)+ ToEol())+ ToEol()">Spaces()+ ToSep("dalign_query_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.hmmpfam-module.html#domain_alignment" class="summary-name">domain_alignment</a> = <code title="domain_align_header+ Rep1(Opt(rf_line)+ domain_align_top+ domain_align\
_middle+ domain_align_bottom)">domain_align_header+ Rep1(Opt(rf_line)+ dom<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_end"></a><span class="summary-name">record_end</span> = <code title="Str("//")+ AnyEol()">Str("//")+ AnyEol()</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.hmmpfam-module.html#record" class="summary-name">record</a> = <code title="Std.record(Rep(sequence_info+ family_header+(no_hit_line | Rep1(family\
_hit_line))+ domain_header+(no_hit_line | Rep1(domain_hit_line))+ alig\
nment_header+(no_hit_line | Rep1(domain_alignment))+ record_end))">Std.record(Rep(sequence_info+ family_header+(no_hit_l<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.hmmpfam-module.html#format" class="summary-name">format</a> = <code title="HeaderFooter("hmmpfam", {}, header, RecordReader.CountLines, (8,), rec\
ord, RecordReader.EndsWith, ("//\n",), None, None, None)">HeaderFooter("hmmpfam", {}, header, RecordReader.Coun<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.hmmpfam-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'>,
13): 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>
</tr>
</table>
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</tr>
</table>
<a name="program_description"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">program_description</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.application_name(Str("hmmpfam"))+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="program_version"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">program_version</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str("HMMER ")+ Std.application_version(Re(r"\d\.\d\w") | Re(r"\d\.\d\.<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
\d"))+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="files"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">files</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
ToEol()+ Str("HMM file:")+ Spaces()+ Std.database_name(UntilEol())+ An<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
yEol()+ Str("Sequence file:")+ Spaces()+ Group("inputfile_name", Until<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Eol())+ AnyEol()+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.search_header(program_description+ program_version+ copyright+ fil<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
es)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="sequence_info"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">sequence_info</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
ToEol()+ Str("Query sequence:")+ Spaces()+ Group("query_name", UntilEo<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
l())+ AnyEol()+ Str("Accession:")+ Spaces()+ Group("query_accession", <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
UntilEol())+ AnyEol()+ Str("Description:")+ Spaces()+ Std.query_descri<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ption(UntilEol())+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="family_header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">family_header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
ToEol()+ Str("Scores")+ ToEol()+ Str("Model")+ ToEol()+ Str("-----")+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="no_hit_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">no_hit_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Spaces()+ Str("[no hits above thresholds]")+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="family_hit_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">family_hit_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("family_model", model_name)+ Spaces()+ ToEol("family_information<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="domain_header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">domain_header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
ToEol()+ Str("Parsed for domains:")+ AnyEol()+ Str("Model")+ ToEol()+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Str("-----")+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="domain_hit_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">domain_hit_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("domain_model", model_name)+ Spaces()+ Group("domain_domain", In<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
teger()+ Str("/")+ Integer())+ Spaces()+ Integer("domain_seq-f")+ Spac<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
es()+ Integer("domain_seq-r")+ Spaces()+ Group("domain_seq_symbols", m<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
atch_symbols)+ Spaces()+ Integer("domain_hmm-f")+ Spaces()+ Integer("d<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
omain_hmm-t")+ Spaces()+ Group("domain_hmm_symbols", match_symbols)+ S<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
paces()+ Float("domain_score")+ Spaces()+ Float("domain_evalue")+ AnyE<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="alignment_header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">alignment_header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
ToEol()+ Str("Alignments of top-scoring domains:")+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="domain_align_header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">domain_align_header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("dalign_name", model_name)+ Str(": domain ")+ Integer("dalign_of<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_domain")+ Str(" of ")+ Integer("dalign_total_domain")+ Str(", from ")<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
+ Integer("dalign_domain_start")+ Str(" to ")+ Integer("dalign_domain_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
end")+ Str(": score ")+ Float("dalign_score")+ Str(", E = ")+ Float("d<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
align_evalue")+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="domain_align_top"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">domain_align_top</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Spaces()+ UntilEol("dalign_match_top")+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="domain_align_middle"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">domain_align_middle</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Spaces()+ UntilEol("dalign_match_middle")+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="domain_align_bottom"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">domain_align_bottom</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Spaces()+ ToSep("dalign_query_name", " ")+ Spaces()+ Alt(Integer("dali<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
gn_query_start")+ Spaces()+ Group("dalign_match_bottom", Re("[\w\-]+")<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ Spaces()+ Integer("dalign_query_end")+ Spaces()+ AnyEol(), Str("- "<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ ToEol())+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="domain_alignment"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">domain_alignment</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
domain_align_header+ Rep1(Opt(rf_line)+ domain_align_top+ domain_align<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_middle+ domain_align_bottom)
</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">
Std.record(Rep(sequence_info+ family_header+(no_hit_line | Rep1(family<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_hit_line))+ domain_header+(no_hit_line | Rep1(domain_hit_line))+ alig<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
nment_header+(no_hit_line | Rep1(domain_alignment))+ record_end))
</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">
HeaderFooter("hmmpfam", {}, header, RecordReader.CountLines, (8,), rec<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ord, RecordReader.EndsWith, ("//\n",), None, None, None)
</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>
13<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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