Raw content of Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Gene3d
<![CDATA[# Author: Marc Sohrmann (ms2@sanger.ac.uk)
# Copyright (c) Marc Sohrmann, 2001
# based on Michelle Clamp's Blast.pm
# 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::Genes3d
=head1 SYNOPSIS
# something like this
my $query = new Bio::Seq(-file => $queryfile,
-format => 'Fasta');
my $hmm = Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Genes3d->new
('-query' => $query,
'-program' => 'hmmpfam' or '/usr/local/pubseq/bin/hmmpfam',
'-database' => 'Pfam');
$hmm->workdir ($workdir);
$hmm->run;
my @results = $hmm->output;
=head1 DESCRIPTION
Blast takes a Bio::Seq (or Bio::PrimarySeq) object and runs hmmpfam.
The resulting output file is parsed to produce a set of Bio::EnsEMBL::FeaturePairs.
=head1 CONTACT
Marc Sohrmann: ms2@sanger.ac.uk
=head1 APPENDIX
=cut
package Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Gene3d;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation;
@ISA = qw(Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation);
###################
# analysis methods
###################
=head2 run_program
Title : run_program
Usage : $self->program
Function : makes the system call to program
Example :
Returns :
Args :
Throws :
=cut
sub run_analysis {
my ($self) = @_;
# run program
print STDERR "running ".$self->program." against ".$self->database."\n";
# some of these options require HMMER 2.2g (August 2001)
my @dbfiles = split(/;/,$self->analysis->db_file);
print STDERR "FILENAME: ".$self->queryfile."\n";
my $cmd = $self->program .' '.
'--acc -E 59.5 -A 100 '.
$self->options .' '.
$dbfiles[0] .' '.
$self->queryfile.' > '.
$self->resultsfile;
print STDERR "$cmd\n";
$self->throw ("Error running ".$self->program." on ".$self->filename." against ".$dbfiles[0])
unless ((system ($cmd)) == 0);
}
=head2 parse_results
Title : parse_results
Usage : $self->parse_results ($filename)
Function : parses program output to give a set of features
Example :
Returns :
Args : filename (optional, can be filename, filehandle or pipe, not implemented)
Throws :
=cut
sub parse_results {
my ($self) = @_;
my $filehandle;
my $resfile = $self->resultsfile();
my @fps;
if (-e $resfile) {
if (-z $resfile) {
print STDERR "Genes3D didn't find any hits\n";
return; }
else {
open (CPGOUT, "<$resfile") or $self->throw("Error opening ", $resfile, " \n");#
}
}
#First parse what comes from the ls mode matches. Every match in that case is taken
my $id;
while (<CPGOUT>) {
chomp;
last if /^Alignments of top-scoring domains/;
next if (/^Model/ || /^\-/ || /^$/);
if (/^Query sequence:\s+(\S+)/) {
$id = $1;
}
if (my ($hid, $start, $end, $hstart, $hend, $score, $evalue) = /^(\S+)\s+\S+\s+(\d+)\s+(\d+)\s+\S+\s+(\d+)\s+(\d+)\s+\S+\s+(\S+)\s+(\S+)/) {
my $fp= $self->create_protein_feature($start,$end,$score,$id,$hstart,$hend,$hid,$self->analysis, sprintf("%.3e", $evalue),0);
push @fps,$fp;
}
}
close (CPGOUT);
$self->output(\@fps);
}
1;
]]>