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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.expressions-module.html">Package expressions</a> ::
Module genbank
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module genbank</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.expressions.genbank-pysrc.html">source code</a></span></p>
<p>Martel based parser to read GenBank formatted files.</p>
<p>This is a huge regular regular expression for GenBank, built using the
'regular expressions on steroids' capabilities of Martel.</p>
<p>Documentation for GenBank format that I found:</p>
<p>o GenBank/EMBL feature tables are described at:
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html</p>
<p>o There are also descriptions of different GenBank lines at:
http://www.ibc.wustl.edu/standards/gbrel.txt</p>
<!-- ==================== FUNCTIONS ==================== -->
<a name="section-Functions"></a>
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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 href="Bio.expressions.genbank-module.html#define_block" class="summary-sig-name">define_block</a>(<span class="summary-sig-arg">identifier</span>,
<span class="summary-sig-arg">block_tag</span>,
<span class="summary-sig-arg">block_data</span>,
<span class="summary-sig-arg">std_block_tag</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">std_tag</span>=<span class="summary-sig-default">None</span>)</span><br />
Define a Martel grouping which can parse a block of text.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.expressions.genbank-pysrc.html#define_block">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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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="INDENT"></a><span class="summary-name">INDENT</span> = <code title="12">12</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="FEATURE_KEY_INDENT"></a><span class="summary-name">FEATURE_KEY_INDENT</span> = <code title="5">5</code>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="FEATURE_QUALIFIER_INDENT"></a><span class="summary-name">FEATURE_QUALIFIER_INDENT</span> = <code title="21">21</code>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="blank_space"></a><span class="summary-name">blank_space</span> = <code title="Martel.Spaces()">Martel.Spaces()</code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="small_indent_space"></a><span class="summary-name">small_indent_space</span> = <code title="Martel.Str(" "* 2)">Martel.Str(" "* 2)</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="big_indent_space"></a><span class="summary-name">big_indent_space</span> = <code title="Martel.Str(" "* FEATURE_KEY_INDENT)">Martel.Str(" "* FEATURE_KEY_INDENT)</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.genbank-module.html#qualifier_space" class="summary-name">qualifier_space</a> = <code title="Martel.Str(" "* FEATURE_QUALIFIER_INDENT) | Martel.Str("\t"+ " "*(FEAT\
URE_QUALIFIER_INDENT-8))">Martel.Str(" "* FEATURE_QUALIFIER_INDENT) | <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="locus"></a><span class="summary-name">locus</span> = <code title="Martel.Group("locus", Martel.Re(r"[\w\-]+"))">Martel.Group("locus", Martel.Re(r"[\w\-]+"))</code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="size"></a><span class="summary-name">size</span> = <code title="Martel.Group("size", Martel.Rep1(Martel.Integer()))">Martel.Group("size", Martel.Rep1(Martel.Integer()))</code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="valid_residue_prefixes"></a><span class="summary-name">valid_residue_prefixes</span> = <code title="['ss-', 'ds-', 'ms-']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">ss-</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ds-</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ms-</code><code class="variable-quote">'</code><code class="variable-group">]</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.genbank-module.html#valid_residue_types" class="summary-name">valid_residue_types</a> = <code title="['DNA',
'RNA',
'mRNA',
'tRNA',
'rRNA',
'uRNA',
'scRNA',
'snRNA',
..."><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">DNA</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">RNA</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">mRNA</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">tRNA</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">rRNA</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-ellipsis">...</code></code>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="residue_prefixes"></a><span class="summary-name">residue_prefixes</span> = <code title="map(Martel.Str, valid_residue_prefixes)">map(Martel.Str, valid_residue_prefixes)</code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="residue_types"></a><span class="summary-name">residue_types</span> = <code title="map(Martel.Str, valid_residue_types)">map(Martel.Str, valid_residue_types)</code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.genbank-module.html#residue_type" class="summary-name">residue_type</a> = <code title="Martel.Group("residue_type", Martel.Opt(Martel.Alt(* residue_prefixes)\
)+ Martel.Opt(Martel.Alt(* residue_types))+ Martel.Opt(Martel.Opt(blan\
k_space)+ Martel.Alt(Martel.Str("circular"), Martel.Str("linear"))))">Martel.Group("residue_type", Martel.Opt(Martel.<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="date"></a><span class="summary-name">date</span> = <code title="Martel.Group("date", Martel.Re("[-\w]+"))">Martel.Group("date", Martel.Re("[-\w]+"))</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.genbank-module.html#valid_divisions" class="summary-name">valid_divisions</a> = <code title="['PRI',
'ROD',
'MAM',
'VRT',
'INV',
'PLN',
'BCT',
'RNA',
..."><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">PRI</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ROD</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">MAM</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">VRT</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">INV</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">PLN</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><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="divisions"></a><span class="summary-name">divisions</span> = <code title="map(Martel.Str, valid_divisions)">map(Martel.Str, valid_divisions)</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.genbank-module.html#data_file_division" class="summary-name">data_file_division</a> = <code title="Martel.Group("data_file_division", Martel.Alt(* divisions))">Martel.Group("data_file_division", Martel<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.genbank-module.html#locus_line" class="summary-name">locus_line</a> = <code title="Martel.Group("locus_line", Martel.Str("LOCUS")+ blank_space+ locus+ bl\
ank_space+ size+ blank_space+ Martel.Re("bp|aa")+ blank_space+ Martel.\
Opt(residue_type+ blank_space)+ data_file_division+ blank_space+ date+\
Martel.AnyEol())">Martel.Group("locus_line", Martel.Str("LOCUS")+ b<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.genbank-module.html#definition_block" class="summary-name">definition_block</a> = <code title="define_block("DEFINITION", "definition_block", "definition", Std.descr\
iption_block, Std.description)">define_block("DEFINITION", "definition_bloc<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="accession"></a><span class="summary-name">accession</span> = <code title="Martel.Group("accession", Martel.Re("[\w]+"))">Martel.Group("accession", Martel.Re("[\w]+"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="region"></a><span class="summary-name">region</span> = <code title="Martel.Group("region", Martel.Re("[\d]+..[\d]+"))">Martel.Group("region", Martel.Re("[\d]+..[\d]+"))</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.genbank-module.html#accession_block" class="summary-name">accession_block</a> = <code title="Martel.Group("accession_block", Martel.Str("ACCESSION")+ Martel.Rep1(b\
lank_space+ Martel.Rep1(accession+ Martel.Opt(Martel.Opt(Martel.Str(" \
"))+ Martel.Str("REGION:")+ Martel.Opt(Martel.Str(" "))+ region)+ Mart\
el.Opt(Martel.Str(" ")))+ Martel.AnyEol()))">Martel.Group("accession_block", Martel.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="nid"></a><span class="summary-name">nid</span> = <code title="Martel.Group("nid", Martel.Re("[\w\d]+"))">Martel.Group("nid", Martel.Re("[\w\d]+"))</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.genbank-module.html#nid_line" class="summary-name">nid_line</a> = <code title="Martel.Group("nid_line", Martel.Str("NID")+ blank_space+ nid+ Martel.A\
nyEol())">Martel.Group("nid_line", Martel.Str("NID")+ blank_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 name="pid"></a><span class="summary-name">pid</span> = <code title="Martel.Group("pid", Martel.Re("[\w\d]+"))">Martel.Group("pid", Martel.Re("[\w\d]+"))</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.genbank-module.html#pid_line" class="summary-name">pid_line</a> = <code title="Martel.Group("pid_line", Martel.Str("PID")+ blank_space+ pid+ Martel.A\
nyEol())">Martel.Group("pid_line", Martel.Str("PID")+ blank_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.genbank-module.html#version" class="summary-name">version</a> = <code title="Martel.Group("version", Std.dbid(Martel.Re("[\w\d\.]+"), {"type": "pri\
mary", "dbname": "genbank"}))">Martel.Group("version", Std.dbid(Martel.Re("[\w\d\.]<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.genbank-module.html#gi" class="summary-name">gi</a> = <code title="Martel.Group("gi", Std.dbid(Martel.Re("[\d]+"), {"type": "secondary", \
"dbname": "genbank"}))">Martel.Group("gi", Std.dbid(Martel.Re("[\d]+"), {"type": <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.genbank-module.html#version_line" class="summary-name">version_line</a> = <code title="Martel.Group("version_line", Martel.Str("VERSION")+ blank_space+ versi\
on+ Martel.Opt(blank_space+ Martel.Str("GI:")+ gi)+ Martel.AnyEol())">Martel.Group("version_line", Martel.Str("VERSIO<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.genbank-module.html#db_source_block" class="summary-name">db_source_block</a> = <code title="define_block("DBSOURCE", "db_source_block", "db_source")">define_block("DBSOURCE", "db_source_block", <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.genbank-module.html#keywords_block" class="summary-name">keywords_block</a> = <code title="define_block("KEYWORDS", "keywords_block", "keywords")">define_block("KEYWORDS", "keywords_block", "k<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.genbank-module.html#segment" class="summary-name">segment</a> = <code title="Martel.Group("segment", Martel.Integer("segment_num")+ Martel.Str(" of\
")+ Martel.Integer("segment_total"))">Martel.Group("segment", Martel.Integer("segment_num"<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.genbank-module.html#segment_line" class="summary-name">segment_line</a> = <code title="Martel.Group("segment_line", Martel.Str("SEGMENT ")+ segment+ Mart\
el.AnyEol())">Martel.Group("segment_line", Martel.Str("SEGMEN<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="source_block"></a><span class="summary-name">source_block</span> = <code title="define_block("SOURCE", "source_block", "source")">define_block("SOURCE", "source_block", "source")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="organism"></a><span class="summary-name">organism</span> = <code title="Martel.Group("organism", Martel.ToEol())">Martel.Group("organism", Martel.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.genbank-module.html#taxonomy" class="summary-name">taxonomy</a> = <code title="Martel.Group("taxonomy", Martel.Rep1(blank_space+ Martel.ToEol()))">Martel.Group("taxonomy", Martel.Rep1(blank_space+ M<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.genbank-module.html#organism_block" class="summary-name">organism_block</a> = <code title="Martel.Group("organism_block", Martel.Str(" ORGANISM")+ blank_space+ \
organism+ taxonomy)">Martel.Group("organism_block", Martel.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="reference_num"></a><span class="summary-name">reference_num</span> = <code title="Martel.Group("reference_num", Martel.Re("[\d]+"))">Martel.Group("reference_num", Martel.Re("[\d]+"))</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.genbank-module.html#reference_bases" class="summary-name">reference_bases</a> = <code title="Martel.Group("reference_bases", Martel.Str("(")+ Martel.Re("[;\w\d \R]\
+")+ Martel.Str(")"))">Martel.Group("reference_bases", Martel.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 href="Bio.expressions.genbank-module.html#reference_line" class="summary-name">reference_line</a> = <code title="Martel.Group("reference_line", Martel.Str("REFERENCE")+ blank_space+ r\
eference_num+ Martel.Opt(blank_space+ reference_bases)+ Martel.AnyEol(\
))">Martel.Group("reference_line", Martel.Str("RE<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.genbank-module.html#authors_block" class="summary-name">authors_block</a> = <code title="define_block(" AUTHORS", "authors_block", "authors")">define_block(" AUTHORS", "authors_block", "au<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.genbank-module.html#consrtm_block" class="summary-name">consrtm_block</a> = <code title="define_block(" CONSRTM", "consrtm_block", "consrtm")">define_block(" CONSRTM", "consrtm_block", "co<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="title_block"></a><span class="summary-name">title_block</span> = <code title="define_block(" TITLE", "title_block", "title")">define_block(" TITLE", "title_block", "title")</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.genbank-module.html#journal_block" class="summary-name">journal_block</a> = <code title="define_block(" JOURNAL", "journal_block", "journal")">define_block(" JOURNAL", "journal_block", "jo<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.genbank-module.html#medline_line" class="summary-name">medline_line</a> = <code title="Martel.Group("medline_line", Martel.Str(" MEDLINE ")+ Martel.Intege\
r("medline_id")+ Martel.AnyEol())">Martel.Group("medline_line", Martel.Str(" MEDL<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.genbank-module.html#pubmed_line" class="summary-name">pubmed_line</a> = <code title="Martel.Group("pubmed_line", Martel.Str(" PUBMED ")+ Martel.Integer\
("pubmed_id")+ Martel.AnyEol())">Martel.Group("pubmed_line", Martel.Str(" PUBME<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="remark_block"></a><span class="summary-name">remark_block</span> = <code title="define_block(" REMARK", "remark_block", "remark")">define_block(" REMARK", "remark_block", "remark")</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.genbank-module.html#reference" class="summary-name">reference</a> = <code title="Martel.Group("reference", reference_line+ Martel.Opt(authors_block)+ M\
artel.Opt(consrtm_block)+ Martel.Opt(title_block)+ journal_block+ Mart\
el.Opt(medline_line)+ Martel.Opt(pubmed_line)+ Martel.Opt(remark_block\
))">Martel.Group("reference", reference_line+ Martel.O<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.genbank-module.html#comment_block" class="summary-name">comment_block</a> = <code title="define_block("COMMENT", "comment_block", "comment")">define_block("COMMENT", "comment_block", "comm<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.genbank-module.html#primary_line" class="summary-name">primary_line</a> = <code title="Martel.Group("primary_line", Martel.Str("PRIMARY")+ blank_space+ Marte\
l.Str("TPA_SPAN")+ blank_space+ Martel.Str("PRIMARY_IDENTIFIER")+ blan\
k_space+ Martel.Str("PRIMARY_SPAN")+ blank_space+ Martel.Str("COMP")+ \
Martel.ToEol())">Martel.Group("primary_line", Martel.Str("PRIMAR<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.genbank-module.html#primary_ref_line" class="summary-name">primary_ref_line</a> = <code title="Martel.Group("primary_ref_line", blank_space+ Martel.Re(r"\d+\-\d+")+ \
blank_space+ Martel.Re("[\S]+")+ blank_space+ Martel.Re("\d+\-\d+")+ M\
artel.Opt(blank_space+ Martel.Str("c"))+ Martel.ToEol())">Martel.Group("primary_ref_line", blank_spac<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.genbank-module.html#primary" class="summary-name">primary</a> = <code title="Martel.Group("primary", primary_line+ Martel.Rep1(primary_ref_line))">Martel.Group("primary", primary_line+ Martel.Rep1(pr<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.genbank-module.html#features_line" class="summary-name">features_line</a> = <code title="Martel.Group("features_line", Martel.Str("FEATURES")+ blank_space+ Mar\
tel.Str("Location/Qualifiers")+ Martel.AnyEol())">Martel.Group("features_line", Martel.Str("FEAT<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.genbank-module.html#feature_key" class="summary-name">feature_key</a> = <code title="Martel.Group("feature_key", Martel.Re("[\w'-]+"))">Martel.Group("feature_key", Martel.Re("[\w'-]+"))</code><br />
location = Martel.Group("location",...
</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.genbank-module.html#location" class="summary-name">location</a> = <code title="Martel.Group("location", Std.feature_location(Martel.UntilEol())+ Mart\
el.AnyEol()+ Martel.Rep(qualifier_space+ Martel.AssertNot(Martel.Str("\
/"))+ Std.feature_location(Martel.UntilEol())+ Martel.AnyEol()))">Martel.Group("location", Std.feature_location(Marte<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.genbank-module.html#feature_key_line" class="summary-name">feature_key_line</a> = <code title="Martel.Group("feature_key_line", big_indent_space+ Std.feature_name(fe\
ature_key)+ location)">Martel.Group("feature_key_line", big_indent<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="quote"></a><span class="summary-name">quote</span> = <code title="Martel.Str('"')">Martel.Str('"')</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.genbank-module.html#quoted_chars" class="summary-name">quoted_chars</a> = <code title="Std.feature_qualifier_description(Martel.Re(r'([^"\R]|"")*'))">Std.feature_qualifier_description(Martel.Re(r'(<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.genbank-module.html#quoted_string" class="summary-name">quoted_string</a> = <code title="quote+ quoted_chars+ Martel.Rep(Martel.AnyEol()+ qualifier_space+ quot\
ed_chars)+ quote+ Martel.AnyEol()">quote+ quoted_chars+ Martel.Rep(Martel.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 href="Bio.expressions.genbank-module.html#unquoted_string" class="summary-name">unquoted_string</a> = <code title="Martel.AssertNot(quote)+ Std.feature_qualifier_description(Martel.Unti\
lEol())+ Martel.AnyEol()">Martel.AssertNot(quote)+ Std.feature_qualifi<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.genbank-module.html#qualifier" class="summary-name">qualifier</a> = <code title="Std.feature_qualifier(qualifier_space+ Martel.Str("/")+ Std.feature_qu\
alifier_name(Martel.Word("feature_qualifier_name"))+(Martel.AnyEol() |\
(Martel.Str("=")+ Martel.Group("feature_qualifier_description", (unquo\
ted_string | quoted_string)))))">Std.feature_qualifier(qualifier_space+ Martel.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="feature"></a><span class="summary-name">feature</span> = <code title="Std.feature(feature_key_line+ Martel.Rep(qualifier))">Std.feature(feature_key_line+ Martel.Rep(qualifier))</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.genbank-module.html#feature_block" class="summary-name">feature_block</a> = <code title="Std.feature_block(Martel.Rep1(feature), {"location-style": "genbank"})">Std.feature_block(Martel.Rep1(feature), {"loca<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="base_count"></a><span class="summary-name">base_count</span> = <code title="Martel.Group("base_count", Martel.Re("[\w\d ]+"))">Martel.Group("base_count", Martel.Re("[\w\d ]+"))</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.genbank-module.html#base_count_line" class="summary-name">base_count_line</a> = <code title="Martel.Group("base_count_line", Martel.Str("BASE COUNT")+ blank_space+\
base_count+ Martel.AnyEol())">Martel.Group("base_count_line", Martel.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 href="Bio.expressions.genbank-module.html#origin_line" class="summary-name">origin_line</a> = <code title="Martel.Group("origin_line", Martel.Str("ORIGIN")+(Martel.ToEol("origin\
_name") | Martel.AnyEol()))">Martel.Group("origin_line", Martel.Str("ORIGIN")<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="base_number"></a><span class="summary-name">base_number</span> = <code title="Martel.Group("base_number", Martel.Re("[\d]+"))">Martel.Group("base_number", Martel.Re("[\d]+"))</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.genbank-module.html#sequence" class="summary-name">sequence</a> = <code title="Std.sequence(Martel.Group("sequence", Martel.Re("[\w]+")))">Std.sequence(Martel.Group("sequence", Martel.Re("[\<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.genbank-module.html#sequence_plus_spaces" class="summary-name">sequence_plus_spaces</a> = <code title="Martel.Group("sequence_plus_spaces", Martel.Rep1(Martel.Str(" ")+ Mart\
el.Opt(sequence))+ Martel.Opt(Martel.Str(" ")))">Martel.Group("sequence_plus_spaces", Ma<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.genbank-module.html#sequence_line" class="summary-name">sequence_line</a> = <code title="Martel.Group("sequence_line", blank_space+ Martel.Opt(base_number)+ se\
quence_plus_spaces+ Martel.AnyEol())">Martel.Group("sequence_line", blank_space+ Mar<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.genbank-module.html#sequence_entry" class="summary-name">sequence_entry</a> = <code title="Std.sequence_block(Martel.Group("sequence_entry", origin_line+ Martel.\
Rep1(sequence_line)))">Std.sequence_block(Martel.Group("sequence_ent<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.genbank-module.html#contig_location" class="summary-name">contig_location</a> = <code title="Martel.Group("contig_location", Martel.ToEol("feature_location")+ Mart\
el.Rep(Martel.Str(" "* INDENT)+ Martel.Re("(?!/)")+ Martel.ToEol("feat\
ure_location")))">Martel.Group("contig_location", Martel.ToEol<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.genbank-module.html#contig_block" class="summary-name">contig_block</a> = <code title="Martel.Group("contig_block", Martel.Str("CONTIG")+ blank_space+ contig\
_location)">Martel.Group("contig_block", Martel.Str("CONTIG<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.genbank-module.html#record_end" class="summary-name">record_end</a> = <code title="Martel.Group("record_end", Martel.Str("//")+ Martel.Rep1(Martel.AnyEol\
()))">Martel.Group("record_end", Martel.Str("//")+ Mart<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.genbank-module.html#record" class="summary-name">record</a> = <code title="Std.record(Martel.Group("genbank_record", locus_line+ definition_block\
+ accession_block+ Martel.Opt(nid_line)+ Martel.Opt(pid_line)+ Martel.\
Opt(version_line)+ Martel.Opt(db_source_block)+ keywords_block+ Martel\
.Opt(segment_line)+ source_block+ organism_block+ Martel.Rep(reference\
)+ Martel.Opt(primary)+ Martel.Opt(comment_block)+ features_line+ feat\
ure_block+ Martel.Alt(Martel.Opt(base_count_line)+ sequence_entry, con\
tig_block)+ record_end))">Std.record(Martel.Group("genbank_record", locus_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.genbank-module.html#header" class="summary-name">header</a> = <code title="Martel.Re("""\
(?P<filename>[^ ]+) +Genetic Sequence Data Bank
*(?P<release_day>\d+) (?P<release_month>\w+) (?P<release_year>\d+)
*(?P<data_bank_name>[^\R]+)
*(?P<data_bank_name>[^\R]+)
...">Martel.Re("<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.genbank-module.html#ncbi_format" class="summary-name">ncbi_format</a> = <code title="Martel.HeaderFooter("genbank", {"format": "ncbi_genbank"}, header, Rec\
ordReader.CountLines, (10,), record, RecordReader.EndsWith, ("//",), N\
one, None, None,)">Martel.HeaderFooter("genbank", {"format": "ncbi_<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.genbank-module.html#format" class="summary-name">format</a> = <code title="Martel.ParseRecords("genbank", {"format": "genbank"}, record, RecordRe\
ader.StartsWith, ("LOCUS ",))">Martel.ParseRecords("genbank", {"format": "genbank"},<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.genbank-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'>,
16): 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>
<!-- ==================== FUNCTION DETAILS ==================== -->
<a name="section-FunctionDetails"></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">Function Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-FunctionDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="define_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">define_block</span>(<span class="sig-arg">identifier</span>,
<span class="sig-arg">block_tag</span>,
<span class="sig-arg">block_data</span>,
<span class="sig-arg">std_block_tag</span>=<span class="sig-default">None</span>,
<span class="sig-arg">std_tag</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.expressions.genbank-pysrc.html#define_block">source code</a></span>
</td>
</tr></table>
<p>Define a Martel grouping which can parse a block of text.</p>
<p>Many of the GenBank lines we'll want to process are grouped into a
block like:</p>
<p>IDENTIFIER Blah blah blah</p>
<p>Where blah blah blah can wrap for multiple lines. This function makes
it easy to consistently define a definition for these blocks.</p>
<p>Arguments: o identifier - The identifier that begins the block (like
DEFINITION). o block_tag - A callback tag for the entire block. o
block_data - A callback tag for the data in the block (ie. the stuff you
are interested in). o std_block_tag - A Bio.Std Martel tag used to
register the entire block as having being a "standard" type of
information. o std_tag - A Bio.Std Martel tag used to register just the
information in the block as being "standard"</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== 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>
</td>
</tr>
</table>
<a name="qualifier_space"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">qualifier_space</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Str(" "* FEATURE_QUALIFIER_INDENT) | Martel.Str("\t"+ " "*(FEAT<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
URE_QUALIFIER_INDENT-8))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="valid_residue_types"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">valid_residue_types</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">DNA</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">RNA</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">mRNA</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">tRNA</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">rRNA</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">uRNA</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">scRNA</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">snRNA</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-ellipsis">...</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="residue_type"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">residue_type</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("residue_type", Martel.Opt(Martel.Alt(* residue_prefixes)<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ Martel.Opt(Martel.Alt(* residue_types))+ Martel.Opt(Martel.Opt(blan<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
k_space)+ Martel.Alt(Martel.Str("circular"), Martel.Str("linear"))))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="valid_divisions"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">valid_divisions</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">PRI</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ROD</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">MAM</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">VRT</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">INV</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">PLN</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">BCT</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">RNA</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-ellipsis">...</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="data_file_division"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">data_file_division</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("data_file_division", Martel.Alt(* divisions))
</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">
Martel.Group("locus_line", Martel.Str("LOCUS")+ blank_space+ locus+ bl<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ank_space+ size+ blank_space+ Martel.Re("bp|aa")+ blank_space+ Martel.<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Opt(residue_type+ blank_space)+ data_file_division+ blank_space+ date+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Martel.AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="definition_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">definition_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
define_block("DEFINITION", "definition_block", "definition", Std.descr<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
iption_block, Std.description)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="accession_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">accession_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("accession_block", Martel.Str("ACCESSION")+ Martel.Rep1(b<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
lank_space+ Martel.Rep1(accession+ Martel.Opt(Martel.Opt(Martel.Str(" <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"))+ Martel.Str("REGION:")+ Martel.Opt(Martel.Str(" "))+ region)+ Mart<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
el.Opt(Martel.Str(" ")))+ Martel.AnyEol()))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="nid_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">nid_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("nid_line", Martel.Str("NID")+ blank_space+ nid+ Martel.A<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
nyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="pid_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">pid_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("pid_line", Martel.Str("PID")+ blank_space+ pid+ Martel.A<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
nyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="version"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">version</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("version", Std.dbid(Martel.Re("[\w\d\.]+"), {"type": "pri<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
mary", "dbname": "genbank"}))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="gi"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">gi</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("gi", Std.dbid(Martel.Re("[\d]+"), {"type": "secondary", <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"dbname": "genbank"}))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="version_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">version_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("version_line", Martel.Str("VERSION")+ blank_space+ versi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
on+ Martel.Opt(blank_space+ Martel.Str("GI:")+ gi)+ Martel.AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="db_source_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">db_source_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
define_block("DBSOURCE", "db_source_block", "db_source")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="keywords_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">keywords_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
define_block("KEYWORDS", "keywords_block", "keywords")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="segment"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">segment</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("segment", Martel.Integer("segment_num")+ Martel.Str(" of<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
")+ Martel.Integer("segment_total"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="segment_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">segment_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("segment_line", Martel.Str("SEGMENT ")+ segment+ Mart<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
el.AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="taxonomy"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">taxonomy</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("taxonomy", Martel.Rep1(blank_space+ Martel.ToEol()))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="organism_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">organism_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("organism_block", Martel.Str(" ORGANISM")+ blank_space+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
organism+ taxonomy)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reference_bases"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reference_bases</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("reference_bases", Martel.Str("(")+ Martel.Re("[;\w\d \R]<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
+")+ Martel.Str(")"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reference_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reference_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("reference_line", Martel.Str("REFERENCE")+ blank_space+ r<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
eference_num+ Martel.Opt(blank_space+ reference_bases)+ Martel.AnyEol(<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="authors_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">authors_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
define_block(" AUTHORS", "authors_block", "authors")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="consrtm_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">consrtm_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
define_block(" CONSRTM", "consrtm_block", "consrtm")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="journal_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">journal_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
define_block(" JOURNAL", "journal_block", "journal")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="medline_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">medline_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("medline_line", Martel.Str(" MEDLINE ")+ Martel.Intege<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
r("medline_id")+ Martel.AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="pubmed_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">pubmed_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("pubmed_line", Martel.Str(" PUBMED ")+ Martel.Integer<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
("pubmed_id")+ Martel.AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reference"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reference</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("reference", reference_line+ Martel.Opt(authors_block)+ M<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
artel.Opt(consrtm_block)+ Martel.Opt(title_block)+ journal_block+ Mart<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
el.Opt(medline_line)+ Martel.Opt(pubmed_line)+ Martel.Opt(remark_block<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="comment_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">comment_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
define_block("COMMENT", "comment_block", "comment")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="primary_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">primary_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("primary_line", Martel.Str("PRIMARY")+ blank_space+ Marte<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
l.Str("TPA_SPAN")+ blank_space+ Martel.Str("PRIMARY_IDENTIFIER")+ blan<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
k_space+ Martel.Str("PRIMARY_SPAN")+ blank_space+ Martel.Str("COMP")+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Martel.ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="primary_ref_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">primary_ref_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("primary_ref_line", blank_space+ Martel.Re(r"\d+\-\d+")+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
blank_space+ Martel.Re("[\S]+")+ blank_space+ Martel.Re("\d+\-\d+")+ M<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
artel.Opt(blank_space+ Martel.Str("c"))+ Martel.ToEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="primary"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">primary</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("primary", primary_line+ Martel.Rep1(primary_ref_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="features_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">features_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("features_line", Martel.Str("FEATURES")+ blank_space+ Mar<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
tel.Str("Location/Qualifiers")+ Martel.AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="feature_key"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">feature_key</h3>
<pre class="literalblock">
location = Martel.Group("location",
Martel.ToEol("feature_location") + Martel.Rep(qualifier_space + Martel.Re("(?!/)") + Martel.ToEol("feature_location")))
</pre>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("feature_key", Martel.Re("[\w'-]+"))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="location"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">location</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("location", Std.feature_location(Martel.UntilEol())+ Mart<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
el.AnyEol()+ Martel.Rep(qualifier_space+ Martel.AssertNot(Martel.Str("<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
/"))+ Std.feature_location(Martel.UntilEol())+ Martel.AnyEol()))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="feature_key_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">feature_key_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("feature_key_line", big_indent_space+ Std.feature_name(fe<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ature_key)+ location)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="quoted_chars"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">quoted_chars</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.feature_qualifier_description(Martel.Re(r'([^"\R]|"")*'))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="quoted_string"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">quoted_string</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
quote+ quoted_chars+ Martel.Rep(Martel.AnyEol()+ qualifier_space+ quot<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ed_chars)+ quote+ Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="unquoted_string"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">unquoted_string</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.AssertNot(quote)+ Std.feature_qualifier_description(Martel.Unti<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
lEol())+ Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="qualifier"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">qualifier</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.feature_qualifier(qualifier_space+ Martel.Str("/")+ Std.feature_qu<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
alifier_name(Martel.Word("feature_qualifier_name"))+(Martel.AnyEol() |<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
(Martel.Str("=")+ Martel.Group("feature_qualifier_description", (unquo<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ted_string | quoted_string)))))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="feature_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">feature_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.feature_block(Martel.Rep1(feature), {"location-style": "genbank"})
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="base_count_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">base_count_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("base_count_line", Martel.Str("BASE COUNT")+ blank_space+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
base_count+ Martel.AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="origin_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">origin_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("origin_line", Martel.Str("ORIGIN")+(Martel.ToEol("origin<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_name") | Martel.AnyEol()))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="sequence"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">sequence</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.sequence(Martel.Group("sequence", Martel.Re("[\w]+")))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="sequence_plus_spaces"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">sequence_plus_spaces</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("sequence_plus_spaces", Martel.Rep1(Martel.Str(" ")+ Mart<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
el.Opt(sequence))+ Martel.Opt(Martel.Str(" ")))
</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">
Martel.Group("sequence_line", blank_space+ Martel.Opt(base_number)+ se<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
quence_plus_spaces+ Martel.AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="sequence_entry"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">sequence_entry</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.sequence_block(Martel.Group("sequence_entry", origin_line+ Martel.<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Rep1(sequence_line)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="contig_location"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">contig_location</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("contig_location", Martel.ToEol("feature_location")+ Mart<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
el.Rep(Martel.Str(" "* INDENT)+ Martel.Re("(?!/)")+ Martel.ToEol("feat<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ure_location")))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="contig_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">contig_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("contig_block", Martel.Str("CONTIG")+ blank_space+ contig<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_location)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="record_end"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">record_end</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("record_end", Martel.Str("//")+ Martel.Rep1(Martel.AnyEol<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
()))
</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(Martel.Group("genbank_record", locus_line+ definition_block<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
+ accession_block+ Martel.Opt(nid_line)+ Martel.Opt(pid_line)+ Martel.<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Opt(version_line)+ Martel.Opt(db_source_block)+ keywords_block+ Martel<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
.Opt(segment_line)+ source_block+ organism_block+ Martel.Rep(reference<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ Martel.Opt(primary)+ Martel.Opt(comment_block)+ features_line+ feat<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ure_block+ Martel.Alt(Martel.Opt(base_count_line)+ sequence_entry, con<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
tig_block)+ record_end))
</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">
Martel.Re("""\
(?P<filename>[^ ]+) +Genetic Sequence Data Bank
*(?P<release_day>\d+) (?P<release_month>\w+) (?P<release_year>\d+)
*(?P<data_bank_name>[^\R]+)
*(?P<data_bank_name>[^\R]+)
<code class="variable-ellipsis">...</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="ncbi_format"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">ncbi_format</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.HeaderFooter("genbank", {"format": "ncbi_genbank"}, header, Rec<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ordReader.CountLines, (10,), record, RecordReader.EndsWith, ("//",), N<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
one, None, None,)
</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">
Martel.ParseRecords("genbank", {"format": "genbank"}, record, RecordRe<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ader.StartsWith, ("LOCUS ",))
</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>
16<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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