Ace::Sequence::GappedAlignment3pm

Usage

    # open database connection and get an Ace::Sequence object
    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 gapped alignments
    @alignments = $seq->alignments('EST_GENOME');
    # get the aligned segments from the first one
    @segs = $alignments[0]->segments;
    # get the position of the first aligned segment on the
    # source sequence:
    ($s_start,$s_end) = ($segs[0]->start,$segs[0]->end);
    # get the target position for the first aligned segment
    ($t_start,$t_end) = ($segs[0]->target->start,$segs[0]->target->end);

Overview

Ace::Sequence::GappedAlignment is a subclass of Ace::Sequence::Feature. It inherits all the methods of Ace::Sequence::Feature, but adds the ability to retrieve the positions of the aligned segments. Each segment is an Ace::Sequence::Feature, from which you can retrieve the source and target coordinates.

Object creation

You will not ordinarily create an Ace::Sequence::GappedAlignment object directly. Instead, objects will be created in response to a alignments() call to an Ace::Sequence object.

Object methods

Most methods are inherited from Ace::Sequence::Feature. The following methods are also supported:

segments()

  @segments = $gene->segments;

Return a list of Ace::Sequence::Feature objects corresponding to similar segments.

relative()

  $relative = $gene->relative;
  $gene->relative(1);

This turns on and off relative coordinates. By default, the exons and intron features will be returned in the coordinate system used by the gene. If relative() is set to a true value, then coordinates will be expressed as relative to the start of the gene. The first exon will (usually) be 1.

Pod errors

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Around line 166:

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