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<title>Ace::Sequence::Feature - Examine Sequence Feature Tables</title>
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<li><a href="#name">NAME</a></li>
<li><a href="#synopsis">SYNOPSIS</a></li>
<li><a href="#description">DESCRIPTION</a></li>
<li><a href="#object_creation">OBJECT CREATION</a></li>
<li><a href="#object_methods">OBJECT METHODS</a></li>
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<h1><a name="name">NAME</a></h1>
<p>Ace::Sequence::Feature - Examine Sequence Feature Tables</p>
<p>
</p>
<hr />
<h1><a name="synopsis">SYNOPSIS</a></h1>
<pre>
# open database connection and get an Ace::Object sequence
use Ace::Sequence;</pre>
<pre>
# get a megabase from the middle of chromosome I
$seq = Ace::Sequence->new(-name => 'CHROMOSOME_I,
-db => $db,
-offset => 3_000_000,
-length => 1_000_000);</pre>
<pre>
# get all the homologies (a list of Ace::Sequence::Feature objs)
@homol = $seq->features('Similarity');</pre>
<pre>
# Get information about the first one
$feature = $homol[0];
$type = $feature->type;
$subtype = $feature->subtype;
$start = $feature->start;
$end = $feature->end;
$score = $feature->score;</pre>
<pre>
# Follow the target
$target = $feature->info;</pre>
<pre>
# print the target's start and end positions
print $target->start,'-',$target->end, "\n";</pre>
<p>
</p>
<hr />
<h1><a name="description">DESCRIPTION</a></h1>
<p><em>Ace::Sequence::Feature</em> is a subclass of <a href="/AcePerl/docs/./Ace/Sequence/Feature.html">the Ace::Sequence::Feature manpage</a>
specialized for returning information about particular features in a
GFF format feature table.</p>
<p>
</p>
<hr />
<h1><a name="object_creation">OBJECT CREATION</a></h1>
<p>You will not ordinarily create an <em>Ace::Sequence::Feature</em> object
directly. Instead, objects will be created in response to a <a href="#feature"><code>feature()</code></a>
call to an <em>Ace::Sequence</em> object. If you wish to create an
<em>Ace::Sequence::Feature</em> object directly, please consult the source
code for the <em>new()</em> method.</p>
<p>
</p>
<hr />
<h1><a name="object_methods">OBJECT METHODS</a></h1>
<p>Most methods are inherited from <em>Ace::Sequence</em>. The following
methods are also supported:</p>
<dl>
<dt><strong><a name="seqname" class="item"><code>seqname()</code></a></strong>
<dd>
<pre>
$object = $feature->seqname;</pre>
</dd>
<dd>
<p>Return the ACeDB Sequence object that this feature is attached to.
The return value is an <em>Ace::Object</em> of the Sequence class. This
corresponds to the first field of the GFF format and does not
necessarily correspond to the <em>Ace::Sequence</em> object from which the
feature was obtained (use <code>source_seq()</code> for that).</p>
</dd>
<dt><strong><a name="source" class="item"><code>source()</code></a></strong>
<dt><strong><a name="method" class="item"><code>method()</code></a></strong>
<dt><strong><a name="subtype" class="item"><code>subtype()</code></a></strong>
<dd>
<pre>
$source = $feature->source;</pre>
</dd>
<dd>
<p>These three methods are all synonyms for the same thing. They return
the second field of the GFF format, called "source" in the
documentation. This is usually the method or algorithm used to
predict the feature, such as "GeneFinder" or "tRNA" scan. To avoid
ambiguity and enhance readability, the <a href="#method"><code>method()</code></a> and <a href="#subtype"><code>subtype()</code></a> synonyms
are also recognized.</p>
</dd>
<dt><strong><a name="feature" class="item"><code>feature()</code></a></strong>
<dt><strong><a name="type" class="item"><code>type()</code></a></strong>
<dd>
<pre>
$type = $feature->type;</pre>
</dd>
<dd>
<p>These two methods are also synonyms. They return the type of the
feature, such as "exon", "similarity" or "Predicted_gene". In the GFF
documentation this is called the "feature" field. For readability,
you can also use <a href="#type"><code>type()</code></a> to fetch the field.</p>
</dd>
<dt><strong><a name="abs_start" class="item"><code>abs_start()</code></a></strong>
<dd>
<pre>
$start = $feature->abs_start;</pre>
</dd>
<dd>
<p>This method returns the absolute start of the feature within the
sequence segment indicated by <a href="#seqname"><code>seqname()</code></a>. As in the <em>Ace::Sequence</em>
method, use <code>start()</code> to obtain the start of the feature relative to its
source.</p>
</dd>
<dt><strong><code>abs_start()</code></strong>
<dd>
<pre>
$start = $feature->abs_start;</pre>
</dd>
<dd>
<p>This method returns the start of the feature relative to the sequence
segment indicated by <a href="#seqname"><code>seqname()</code></a>. As in the <em>Ace::Sequence</em> method,
you will more usually use the inherited <code>start()</code> method to obtain the
start of the feature relative to its source sequence (the
<em>Ace::Sequence</em> from which it was originally derived).</p>
</dd>
<dt><strong><a name="abs_end" class="item"><code>abs_end()</code></a></strong>
<dd>
<pre>
$start = $feature->abs_end;</pre>
</dd>
<dd>
<p>This method returns the end of the feature relative to the sequence
segment indicated by <a href="#seqname"><code>seqname()</code></a>. As in the <em>Ace::Sequence</em> method,
you will more usually use the inherited <code>end()</code> method to obtain the end
of the feature relative to the <em>Ace::Sequence</em> from which it was
derived.</p>
</dd>
<dt><strong><a name="score" class="item"><code>score()</code></a></strong>
<dd>
<pre>
$score = $feature->score;</pre>
</dd>
<dd>
<p>For features that are associated with a numeric score, such as
similarities, this returns that value. For other features, this
method returns undef.</p>
</dd>
<dt><strong><a name="strand" class="item"><code>strand()</code></a></strong>
<dd>
<pre>
$strand = $feature->strand;</pre>
</dd>
<dd>
<p>Returns the strandedness of this feature, either "+1" or "-1". For
features that are not stranded, returns 0.</p>
</dd>
<dt><strong><a name="reversed" class="item"><code>reversed()</code></a></strong>
<dd>
<pre>
$reversed = $feature->reversed;</pre>
</dd>
<dd>
<p>Returns true if the feature is reversed relative to its source
sequence.</p>
</dd>
<dt><strong><a name="frame" class="item"><code>frame()</code></a></strong>
<dd>
<pre>
$frame = $feature->frame;</pre>
</dd>
<dd>
<p>For features that have a frame, such as a predicted coding sequence,
returns the frame, either 0, 1 or 2. For other features, returns undef.</p>
</dd>
<dt><strong><a name="group" class="item"><code>group()</code></a></strong>
<dt><strong><a name="info" class="item"><code>info()</code></a></strong>
<dt><strong><a name="target" class="item"><code>target()</code></a></strong>
<dd>
<pre>
$info = $feature->info;</pre>
</dd>
<dd>
<p>These methods (synonyms for one another) return an Ace::Object
containing other information about the feature derived from the 8th
field of the GFF format, the so-called "group" field. The type of the
Ace::Object is dependent on the nature of the feature. The
possibilities are shown in the table below:</p>
</dd>
<dd>
<pre>
Feature Type Value of Group Field
------------ --------------------
note A Text object containing the note.
similarity An Ace::Sequence::Homology object containing
the target and its start/stop positions.</pre>
</dd>
<dd>
<pre>
intron An Ace::Object containing the gene from
exon which the feature is derived.
misc_feature</pre>
</dd>
<dd>
<pre>
other A Text object containing the group data.</pre>
</dd>
<dt><strong><a name="asstring" class="item"><code>asString()</code></a></strong>
<dd>
<pre>
$label = $feature->asString;</pre>
</dd>
<dd>
<p>Returns a human-readable identifier describing the nature of the
feature. The format is:</p>
</dd>
<dd>
<pre>
$type:$name/$start-$end</pre>
</dd>
<dd>
<p>for example:</p>
</dd>
<dd>
<pre>
exon:ZK154.3/1-67</pre>
</dd>
<dd>
<p>This method is also called automatically when the object is treated in
a string context.</p>
</dd>
</dl>
<p>
</p>
<hr />
<h1><a name="see_also">SEE ALSO</a></h1>
<p><a href="/AcePerl/docs/./Ace.html">the Ace manpage</a>, <a href="/AcePerl/docs/./Ace/Object.html">the Ace::Object manpage</a>, <a href="/AcePerl/docs/./Ace/Sequence.html">the Ace::Sequence manpage</a>,<a href="/AcePerl/docs/./Ace/Sequence/Homol.html">the Ace::Sequence::Homol manpage</a>,
<a href="/AcePerl/docs/./Ace/Sequence/FeatureList.html">the Ace::Sequence::FeatureList manpage</a>, <em>GFF</em></p>
<p>
</p>
<hr />
<h1><a name="author">AUTHOR</a></h1>
<p>Lincoln Stein <<a href="mailto:lstein@cshl.org">lstein@cshl.org</a>> with extensive help from Jean
Thierry-Mieg <<a href="mailto:mieg@kaa.crbm.cnrs-mop.fr">mieg@kaa.crbm.cnrs-mop.fr</a>></p>
<p>Copyright (c) 1999, Lincoln D. Stein</p>
<p>This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.</p>
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