Ace::Sequence::Feature - Examine Sequence Feature Tables
# open database connection and get an Ace::Object sequence use Ace::Sequence;
# 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);
# get all the homologies (a list of Ace::Sequence::Feature objs) @homol = $seq->features('Similarity');
# Get information about the first one $feature = $homol[0]; $type = $feature->type; $subtype = $feature->subtype; $start = $feature->start; $end = $feature->end; $score = $feature->score;
# Follow the target $target = $feature->info;
# print the target's start and end positions print $target->start,'-',$target->end, "\n";
Ace::Sequence::Feature is a subclass of the Ace::Sequence::Feature manpage specialized for returning information about particular features in a GFF format feature table.
You will not ordinarily create an Ace::Sequence::Feature object
directly. Instead, objects will be created in response to a feature()
call to an Ace::Sequence object. If you wish to create an
Ace::Sequence::Feature object directly, please consult the source
code for the new() method.
Most methods are inherited from Ace::Sequence. The following methods are also supported:
seqname()
$object = $feature->seqname;
Return the ACeDB Sequence object that this feature is attached to.
The return value is an Ace::Object of the Sequence class. This
corresponds to the first field of the GFF format and does not
necessarily correspond to the Ace::Sequence object from which the
feature was obtained (use source_seq()
for that).
source()
method()
subtype()
$source = $feature->source;
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 method()
and subtype()
synonyms
are also recognized.
feature()
type()
$type = $feature->type;
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 type()
to fetch the field.
abs_start()
$start = $feature->abs_start;
This method returns the absolute start of the feature within the
sequence segment indicated by seqname(). As in the Ace::Sequence
method, use start()
to obtain the start of the feature relative to its
source.
abs_start()
$start = $feature->abs_start;
This method returns the start of the feature relative to the sequence
segment indicated by seqname(). As in the Ace::Sequence method,
you will more usually use the inherited start()
method to obtain the
start of the feature relative to its source sequence (the
Ace::Sequence from which it was originally derived).
abs_end()
$start = $feature->abs_end;
This method returns the end of the feature relative to the sequence
segment indicated by seqname(). As in the Ace::Sequence method,
you will more usually use the inherited end()
method to obtain the end
of the feature relative to the Ace::Sequence from which it was
derived.
score()
$score = $feature->score;
For features that are associated with a numeric score, such as similarities, this returns that value. For other features, this method returns undef.
strand()
$strand = $feature->strand;
Returns the strandedness of this feature, either ``+1'' or ``-1''. For features that are not stranded, returns 0.
reversed()
$reversed = $feature->reversed;
Returns true if the feature is reversed relative to its source sequence.
frame()
$frame = $feature->frame;
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.
group()
info()
target()
$info = $feature->info;
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:
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.
intron An Ace::Object containing the gene from exon which the feature is derived. misc_feature
other A Text object containing the group data.
asString()
$label = $feature->asString;
Returns a human-readable identifier describing the nature of the feature. The format is:
$type:$name/$start-$end
for example:
exon:ZK154.3/1-67
This method is also called automatically when the object is treated in a string context.
the Ace manpage, the Ace::Object manpage, the Ace::Sequence manpage,the Ace::Sequence::Homol manpage, the Ace::Sequence::FeatureList manpage, GFF
Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>
Copyright (c) 1999, Lincoln D. Stein
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.