Raw content of Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Seg
<![CDATA[# Author: Marc Sohrmann (ms2@sanger.ac.uk)
# Copyright (c) Marc Sohrmann, 2001
# You may distribute this code under the same terms as perl itself
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Seg
=head1 SYNOPSIS
my $seqstream = Bio::SeqIO->new ( -file => $queryfile,
-fmt => 'Fasta',
);
$seq = $seqstream->next_seq;
my $seg = Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Seg->new ( -QUERY => $seq);
$seg->workdir ($workdir);
$seg->run;
my @results = $seg->output;
=head1 DESCRIPTION
Seg takes a Bio::Seq (or Bio::PrimarySeq) object
and runs seg on it (detecting low complexity sequences).
The resulting output file is parsed to produce a set of features.
=head1 CONTACT
Marc Sohrmann: ms2@sanger.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _.
=cut
package Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Seg;
use vars qw(@ISA);
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation;
@ISA = qw(Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation);
sub multiprotein{
my ($self) = @_;
return 1;
}
sub run_analysis {
my ($self) = @_;
throw ("Error running ".$self->program." on ".$self->queryfile)
unless ((system ($self->program." ".$self->queryfile." -l > ".
$self->resultsfile)) == 0);
}
sub parse_results {
my ($self) = @_;
my ($fh);
my $resfile = $self->resultsfile;
if (-e $resfile) {
# it's a filename
if (-z $resfile) {
return;
}else {
open($fh, "<$resfile") or throw ("Error opening $resfile");
}
} else {
# it'a a filehandle
$fh = $resfile;
}
# parse
my @pfs;
while (<$fh>) {
chomp;
next if /^$/;
if (/^\>/) {
/^\>(\S+)?\((\d+)\-(\d+)\)\s*complexity=(\S+)/;
my $tid = $1;
my $start = $2;
my $end = $3;
my $score = $4;
my $fp = $self->create_protein_feature($start, $end, $score, $tid,
0, 0, 'Seg',
$self->analysis, 0, 0);
push @pfs, $fp;
}
}
close($fh);
$self->output(\@pfs);
}
=head2 get_low_complexity_length
Title : get_low_complexity_length
Usage : $len = $self->get_low_complexity_length;
Function : returns *percentage* low complexity of protein
Example :
Returns : a percentage_id
Args :
Throws :
Notes : It only makes sense to call this method when the
Runnable was created with a single Bio::Seq
=cut
sub get_low_complexity_length {
my ($self) = @_;
if ($self->query->length > 0) {
my $lc_length = 0;
foreach my $feat (@{$self->output}) {
$lc_length += abs($feat->end - $feat->start) + 1;
}
my $low_complexity = ($lc_length)/($self->query->length);
$low_complexity *= 100;
return $low_complexity;
}
else {
return 0;
}
}
1;
]]>