Raw content of Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Coil
<![CDATA[
=pod
=head1 NAME
Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Coil
=head1 SYNOPSIS
my $seqstream = Bio::SeqIO->new ( -file => $queryfile,
-fmt => 'Fasta',
);
$seq = $seqstream->next_seq;
my $ncoils = Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Coil->new(
-analysis => $ana,
-query => $query);
$ncoils->run;
my @list = @{$ncoils->run}
=head1 DESCRIPTION
=cut
package Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Coil;
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);
sub multiprotein{
my ($self) = @_;
return 1;
}
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
if (not $self->database) {
throw("You must supply the Coils runnable with a database directory");
} elsif (not -d $self->database) {
throw($self->database . " is not a *valid* database directory");
} else {
$ENV{'COILSDIR'} = $self->database;
}
return $self;
}
sub run_analysis {
my ($self) = @_;
my $command = $self->program." -f < ".$self->queryfile." > ".$self->resultsfile;
# run program
throw ("Error running ".$self->program." on ".$self->queryfile)
unless (system($command) == 0);
}
sub parse_results {
my ($self) = @_;
my ($fh, @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;
}
# parse
my $seqio = Bio::SeqIO->new(-format => 'fasta',
-fh => $fh);
while(my $seq = $seqio->next_seq) {
my $pep = $seq->seq;
while ($pep =~ m/(x+)/g) {
my $end = pos($pep);
my $start = $end - length($1) + 1;
my $fp = $self->create_protein_feature($start, $end, 0, $seq->id, 0, 0,
'ncoils', $self->analysis,
0, 0);
push @pfs, $fp;
}
}
$self->output(\@pfs);
}
1;
]]>