Raw content of Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Prodom
<![CDATA[# Author: Gary Williams (gw3@sanger.ac.uk)
# Copyright (c) Gary Williams (2005)
# 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::Prodom
=head1 SYNOPSIS
# something like this
my $query = new Bio::Seq(-file => $queryfile,
-format => 'Fasta');
my $hmm = Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Prodom->new
('-query' => $query,
'-program' => 'hmmpfam' or '/usr/local/pubseq/bin/hmmpfam',
'-database' => 'sf_hmm');
$hmm->workdir ($workdir);
$hmm->run;
my @results = $hmm->output;
=head1 DESCRIPTION
Blast takes a Bio::Seq (or Bio::PrimarySeq) object and runs hmmpfam.
The resulting output file is parsed to produce a set of Bio::EnsEMBL::FeaturePairs.
=head1 CONTACT
Marc Sohrmann: ms2@sanger.ac.uk
=head1 APPENDIX
=cut
package Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Prodom;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::EnsEMBL::Root;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation;
@ISA = qw(Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation);
sub run_analysis {
my ($self) = @_;
# run program
print STDERR "running ".$self->program." against ".$self->database."\n";
my @dbfiles = split(/;/,$self->analysis->db_file); # hmmm ... only the first bit is used
print STDERR "FILENAME: ".$self->queryfile."\n";
my $cmd = $self->program .' '.
$self->options .' '.
'-P ' . '/software/worm/iprscan/bin/binaries/blast/ ' .
'-p ' . 'blastp' . ' '.
'-d ' . $dbfiles[0] .' '.
'-s ' . $self->queryfile . ' '.
'-t ' . '/tmp' . ' '.
'-h 0 -f '.
' >' . $self->resultsfile;
print STDERR "$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 $self->resultsfile) {
print STDERR "Prodom didn't find any hits\n";
return; }
else {
open (CPGOUT, "<$resfile") or $self->throw("Error opening ", $resfile, " \n");#
}
}
#5_Translation_id_5_gene_5 1 40 // pd_PD000035;sp_TLL_DROVI_O16845; 33 102 // S=135 E=2e-08 // (1021) RECEPTOR NUCLEAR TRANSCRIPTION DNA-BINDING REGULATION ZINC-FINGER METAL-BINDING ZINC HORMONE FAMILY Length = 70
# Example output:
#CE27771 203 318 // pd_PD002460;sp_Q19242_CAEEL_Q19242; 199 344 // S=122 E=6e-06 // (189) BIOSYNTHESIS MOLYBDOPTERIN MOEA COFACTOR MOLYBDENUM ENZYME PROBABLE LONG GEPHYRIN DOMAIN Length = 146
#//
while (<CPGOUT>) {
chomp;
if (my ($id, $start, $end, $hid, $hstart, $hend, $score, $evalue) = /^(\S+)\s+(\d+)\s+(\d+)\s+\S+\s+pd_(\S+);\S+\s+(\d+)\s+(\d+)\s+\S+\s+S=(\S+)\s+E=(\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;
]]>