Raw content of Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Tmhmm
<![CDATA[
=pod
=head1 NAME
Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Tmhmm
=head1 SYNOPSIS
my $seqstream = Bio::SeqIO->new ( -file => $clonefile,
-fmt => 'Fasta',
);
$seq = $seqstream->next_seq;
my $tmhmm = Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Tmhmm->new(-analysis => $ana,
-query => $seq,
-modelfile => $mf,
-optionsfile => $o);
$tmhmm->run;
my @results = $tmhmm->output;
=head1 DESCRIPTION
=cut
package Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Tmhmm;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation;
@ISA = qw(Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation);
sub multiprotein{
my ($self) = @_;
return 1;
}
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($options_file,
$model_file) = rearrange(['OPTIONSFILE',
'MODELFILE'
], @args);
throw("You must supply a model file for Tmhmm")
if not defined $model_file;
$self->options_file($options_file)
if defined $options_file;
$self->model_file($model_file);
return $self;
}
sub run_analysis {
my ($self) = @_;
# run program
my $cmd = "cat " . $self->queryfile . " | " . $self->program;
if ($self->options_file) {
$cmd .= " -f " . $self->options_file;
}
if ($self->options) {
$cmd .= " " . $self->options;
}
$cmd .= " -modelfile " . $self->model_file . " > " . $self->resultsfile;
print "Running $cmd\n";
# decodeanhmm returns a non-zero exit status, even when successful
# So we just have to run it and wait until we parse the output
# file to see whether it ran successfully
system($cmd);
}
sub parse_results {
my ($self) = @_;
my ($fh, $id, @pfs);
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;
}
my $id_count = 0;
while (<$fh>) {
chomp;
next if /^$/;
if (/^\>(\S+)/) {
$id = $1;
$id_count++;
}
elsif (/^\%pred/) {
my ($junk, $values) = split /:/;
my @tm = split (/,/, $values);
foreach (@tm) {
/(\w+)\s+(\d+)\s+(\d+)/;
my $orien = $1;
my $start = $2;
my $end = $3;
$orien = uc ($orien);
if ($orien eq "M") {
my $fp = $self->create_protein_feature($start, $end, 0, $id, 0,
0, 'Tmhmm',
$self->analysis, 0, 0);
push @pfs, $fp;
}
}
}
}
close($fh);
throw("Something went wrong when running decodeanhmm; no ids found in output")
if not $id_count;
$self->output(\@pfs);
}
sub model_file {
my ($self, $val) = @_;
if (defined $val) {
$self->{_model_file} = $val;
}
return $self->{_model_file};
}
sub options_file {
my ($self, $val) = @_;
if (defined $val) {
$self->{_options_file} = $val;
}
return $self->{_options_file};
}
1;
]]>