Ace::Sequence::GappedAlignment - Gapped alignment object

AcePerl documentation Contained in the AcePerl distribution.

Index

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NAME

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Ace::Sequence::GappedAlignment - Gapped alignment object

SYNOPSIS

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    # 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);

DESCRIPTION

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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

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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

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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.

SEE ALSO

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Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::Feature, Ace::Sequence::FeatureList, GFF

AUTHOR

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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.

AcePerl documentation Contained in the AcePerl distribution. 
package Ace::Sequence::GappedAlignment;

use strict;
use Ace;
use Ace::Sequence::Feature;
use vars '$AUTOLOAD';
use overload 
  '""' => 'asString',
  'fallback' => 'TRUE';
  ;
use vars '$VERSION';
$VERSION = '1.20';

*sub_SeqFeature = \&merged_segments;


# autoload delegates everything to the Sequence feature
sub AUTOLOAD {
  my($pack,$func_name) = $AUTOLOAD=~/(.+)::([^:]+)$/;
  my $self = shift;
  $self->{base}->$func_name(@_);
}

sub new {
  my $class = shift;
  my $segments = shift;
  my @segments = sort {$a->start <=> $b->start} @$segments;

  # find the min and max for the alignment
  my ($offset,$len);
  if ($segments[0]->start < $segments[-1]->start) {  # positive direction
    $offset = $segments[0]->{offset};
    $len = $segments[-1]->end - $segments[0]->start + 1;
  } else {
    $offset = $segments[-1]->{offset};
    $len = $segments[0]->end - $segments[-1]->start + 1;
  }

  my $base = { %{$segments[0]} };
  $base->{offset} = $offset;
  $base->{length} = $len;

  bless $base,ref($segments[0]);
  return bless {
		base     => $base,
		segments => $segments,
	       },$class;
}

sub smapped { 1; }

sub asString {
  shift->{base}->info;
}

sub type   { return 'similarity'; }

sub relative {
  my $self = shift;
  my $d = $self->{relative};
  $self->{relative} = shift if @_;
  $d;
}

sub segments {
  my $self = shift;
  return $self->{segments} ? @{$self->{segments}} : () unless $self->relative;
  # otherwise, we have to handle relative coordinates
  my $base   = $self->{base};
  my @e = map {Ace::Sequence->new(-refseq=>$base,-seq=>$_)} @{$self->{segments}};
  return $self->strand < 0 ? reverse @e : @e;
}

sub merged_segments {
  my $self = shift;

  return @{$self->{merged_segs}} if exists $self->{merged_segs};

  my @segs = sort {$a->start <=> $b->start} $self->segments;
  # attempt to merge overlapping segments
  my @merged;
  for my $s (@segs) {
    my $previous = $merged[-1];
    if ($previous && $previous->end+1 >= $s->start) {
      $previous->{length} = $s->end - $previous->start + 1;  # extend
    } else {
      my $clone = bless {%$s},ref($s);
      push @merged,$clone;
    }
  }
  $self->{merged_segs} = \@merged;
  return @merged;
}

1;

__END__