Raw content of Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Pfam_wormbase
package Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Pfam_wormbase;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation;
use Env qw(PATH);
@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";
print STDERR "FILENAME: ".$self->queryfile."\n";
my $cmd = $self->program .' '.
$self->analysis->parameters .' '.
'-o ' . $self->resultsfile .' '.
$self->queryfile;
print STDERR "$cmd\n";
$PATH = '/software/worm/bin/hmmer/:/software/worm/iprscan/bin/binaries/:'.$PATH; #for hmmpfam
$PATH = '/software/worm/iprscan/bin/binaries/blast/:'.$PATH; #for blastall
$self->throw ("Error running Pfam_wormbase ".$self->program." on ".$self->queryfile)
unless ((system ($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 $resfile) {
print STDERR "Pfam didn't find any hits\n";
return;
} else {
open (CPGOUT, "<$resfile") or $self->throw("Error opening ", $resfile, " \n"); #
}
}
# Example output for sequence ID 2345:
#2345 279 319 PF00400.23 1 38 13.7 0.008 WD40
#2345 323 361 PF00400.23 1 38 22.0 0.0023 WD40
# now
# 12311 49 288 PF00149.20 1 124 ls 90.9 4.4e-24 Metallophos
# 12311 294 517 PF04152.6 1 240 ls 310.9 2.6e-90 Mre11_DNA_bind
# 11845 1 167 PF06653.3 1 160 ls -12.3 0.00016 DUF1164
my $id;
while () {
chomp;
print "$_\n";
if (my ($id, $start, $end, $hid, $hstart, $hend, $skipit,$score, $evalue) = /^(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(ls)*\s+([\d\.\-\+]+)\s+(\S+)\s+(\S+)/) {
print "matched\n";
my $percentIdentity = 0;
my $fp= $self->create_protein_feature($start, $end, $score, $id, $hstart, $hend, $hid, $self->analysis, $evalue, $percentIdentity);
push @fps, $fp;
}
}
close (CPGOUT);
$self->output(\@fps);
}
1;