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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.GenBank-module.html">Package GenBank</a> ::
<a href="Bio.GenBank.Record-module.html">Module Record</a> ::
Class Record
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Record</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record">source code</a></span></p>
<p>Hold GenBank information in a format similar to the original
record.</p>
<p>The Record class is meant to make data easy to get to when you are
just interested in looking at GenBank data.</p>
<p>Attributes: o locus - The name specified after the LOCUS keyword in
the GenBank record. This may be the accession number, or a clone id or
something else. o size - The size of the record. o residue_type - The
type of residues making up the sequence in this record. Normally
something like RNA, DNA or PROTEIN, but may be as esoteric as 'ss-RNA
circular'. o data_file_division - The division this record is stored
under in GenBank (ie. PLN -> plants; PRI -> humans, primates; BCT
-> bacteria...) o date - The date of submission of the record, in a
form like '28-JUL-1998' o accession - list of all accession numbers for
the sequence. o nid - Nucleotide identifier number. o pid - Proteint
identifier number o version - The accession number + version (ie.
AB01234.2) o db_source - Information about the database the record came
from o gi - The NCBI gi identifier for the record. o keywords - A list of
keywords related to the record. o segment - If the record is one of a
series, this is info about which segment this record is (something like
'1 of 6'). o source - The source of material where the sequence came
from. o organism - The genus and species of the organism (ie. 'Homo
sapiens') o taxonomy - A listing of the taxonomic classification of the
organism, starting general and getting more specific. o references - A
list of Reference objects. o comment - Text with any kind of comment
about the record. o features - A listing of Features making up the
feature table. o base_counts - A string with the counts of bases for the
sequence. o origin - A string specifying info about the origin of the
sequence. o sequence - A string with the sequence itself. o contig - A
string of location information for a CONTIG in a RefSeq file.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record.__init__">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.GenBank.Record.Record-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Provide a GenBank formatted output option for a Record.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record.__str__">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<tr>
<td><span class="summary-sig"><a name="_locus_line"></a><span class="summary-sig-name">_locus_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Provide the output string for the LOCUS line.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._locus_line">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_definition_line"></a><span class="summary-sig-name">_definition_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Provide output for the DEFINITION line.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._definition_line">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_accession_line"></a><span class="summary-sig-name">_accession_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Output for the ACCESSION line.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._accession_line">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_version_line"></a><span class="summary-sig-name">_version_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Output for the VERSION line.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._version_line">source code</a></span>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.GenBank.Record.Record-class.html#_nid_line" class="summary-sig-name" onclick="show_private();">_nid_line</a>(<span class="summary-sig-arg">self</span>)</span><br />
Output for the NID line.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._nid_line">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.GenBank.Record.Record-class.html#_pid_line" class="summary-sig-name" onclick="show_private();">_pid_line</a>(<span class="summary-sig-arg">self</span>)</span><br />
Output for PID line.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._pid_line">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_keywords_line"></a><span class="summary-sig-name">_keywords_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Output for the KEYWORDS line.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._keywords_line">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<td><span class="summary-sig"><a name="_db_source_line"></a><span class="summary-sig-name">_db_source_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Output for DBSOURCE line.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._db_source_line">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_segment_line"></a><span class="summary-sig-name">_segment_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Output for the SEGMENT line.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._segment_line">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_source_line"></a><span class="summary-sig-name">_source_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Output for SOURCE line on where the sample came from.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._source_line">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="_organism_line"></a><span class="summary-sig-name">_organism_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Output for ORGANISM line with taxonomy info.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._organism_line">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_comment_line"></a><span class="summary-sig-name">_comment_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Output for the COMMENT lines.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._comment_line">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_features_line"></a><span class="summary-sig-name">_features_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Output for the FEATURES line.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._features_line">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_base_count_line"></a><span class="summary-sig-name">_base_count_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Output for the BASE COUNT line with base information.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._base_count_line">source code</a></span>
</td>
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</td>
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<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_origin_line"></a><span class="summary-sig-name">_origin_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Output for the ORIGIN line</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._origin_line">source code</a></span>
</td>
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</table>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_sequence_line"></a><span class="summary-sig-name">_sequence_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Output for all of the sequence.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._sequence_line">source code</a></span>
</td>
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</table>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_contig_line"></a><span class="summary-sig-name">_contig_line</span>(<span class="summary-sig-arg">self</span>)</span><br />
Output for CONTIG location information from RefSeq.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._contig_line">source code</a></span>
</td>
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</td>
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</table>
<!-- ==================== CLASS VARIABLES ==================== -->
<a name="section-ClassVariables"></a>
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<td align="left"><span class="table-header">Class Variables</span></td>
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><span class="options">[<a href="#section-ClassVariables"
class="privatelink" onclick="toggle_private();"
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="GB_LINE_LENGTH"></a><span class="summary-name">GB_LINE_LENGTH</span> = <code title="79">79</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="GB_BASE_INDENT"></a><span class="summary-name">GB_BASE_INDENT</span> = <code title="12">12</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="GB_FEATURE_INDENT"></a><span class="summary-name">GB_FEATURE_INDENT</span> = <code title="21">21</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="GB_INTERNAL_INDENT"></a><span class="summary-name">GB_INTERNAL_INDENT</span> = <code title="2">2</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="GB_OTHER_INTERNAL_INDENT"></a><span class="summary-name">GB_OTHER_INTERNAL_INDENT</span> = <code title="3">3</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="GB_FEATURE_INTERNAL_INDENT"></a><span class="summary-name">GB_FEATURE_INTERNAL_INDENT</span> = <code title="5">5</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="GB_SEQUENCE_INDENT"></a><span class="summary-name">GB_SEQUENCE_INDENT</span> = <code title="9">9</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_FORMAT"></a><span class="summary-name">BASE_FORMAT</span> = <code title="'%-12s'"><code class="variable-quote">'</code><code class="variable-string">%-12s</code><code class="variable-quote">'</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="INTERNAL_FORMAT"></a><span class="summary-name">INTERNAL_FORMAT</span> = <code title="' %-10s'"><code class="variable-quote">'</code><code class="variable-string"> %-10s</code><code class="variable-quote">'</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="OTHER_INTERNAL_FORMAT"></a><span class="summary-name">OTHER_INTERNAL_FORMAT</span> = <code title="' %-9s'"><code class="variable-quote">'</code><code class="variable-string"> %-9s</code><code class="variable-quote">'</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_FEATURE_FORMAT"></a><span class="summary-name">BASE_FEATURE_FORMAT</span> = <code title="'%-21s'"><code class="variable-quote">'</code><code class="variable-string">%-21s</code><code class="variable-quote">'</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="INTERNAL_FEATURE_FORMAT"></a><span class="summary-name">INTERNAL_FEATURE_FORMAT</span> = <code title="' %-16s'"><code class="variable-quote">'</code><code class="variable-string"> %-16s</code><code class="variable-quote">'</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="SEQUENCE_FORMAT"></a><span class="summary-name">SEQUENCE_FORMAT</span> = <code title="'%9s'"><code class="variable-quote">'</code><code class="variable-string">%9s</code><code class="variable-quote">'</code></code>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<a name="__str__"></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">__str__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Informal representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record.__str__">source code</a></span>
</td>
</tr></table>
<p>Provide a GenBank formatted output option for a Record.</p>
<p>The objective of this is to provide an easy way to read in a GenBank
record, modify it somehow, and then output it in 'GenBank format.' We are
striving to make this work so that a parsed Record that is output using
this function will look exactly like the original record.</p>
<p>Much of the output is based on format description info at:</p>
<p>ftp://ncbi.nlm.nih.gov/genbank/gbrel.txt</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_nid_line"></a>
<div class="private">
<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">_nid_line</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._nid_line">source code</a></span>
</td>
</tr></table>
<p>Output for the NID line. Use of NID is obsolete in GenBank files.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_pid_line"></a>
<div class="private">
<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">_pid_line</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank.Record-pysrc.html#Record._pid_line">source code</a></span>
</td>
</tr></table>
<p>Output for PID line. Presumedly, PID usage is also obsolete.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
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