Raw content of Bio::EnsEMBL::Pipeline::SeqFetcher::Efetch
<![CDATA[#
# Cared for by EnsEMBL <ensembl-dev@ebi.ac.uk>
#
# Copyright GRL & EBI
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Pipeline::SeqFetcher::Efetch
=head1 SYNOPSIS
my $obj = Bio::EnsEMBL::Pipeline::SeqFetcher::Efetch->new(
'-executable' => $exe,
'-lib' => $lib,
);
my $seq = $obj->get_Seq_by_acc($acc);
=head1 DESCRIPTION
Object to retrieve sequences as Bio::Seq, using efetch.
=head1 CONTACT
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::EnsEMBL::Pipeline::SeqFetcher::Efetch;
use strict;
use Bio::EnsEMBL::Root;
use Bio::DB::RandomAccessI;
use Bio::Seq;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Root Bio::DB::RandomAccessI);
sub new {
my ($class, @args) = @_;
my $self = bless {}, $class;
my ($exe, $lib) = $self->_rearrange([
'EXECUTABLE',
'LIBRARY'], @args);
if (!defined $exe) {
$exe = 'efetch';
}
$self->executable($exe);
if (defined $lib) {
$self->library($lib);
}
return $self; # success - we hope!
}
=head2 executable
Title : executable
Usage : $self->executable('/path/to/executable');
Function: Get/set for the path to the executable being used by the module. If not set, the executable is looked for in $PATH.
Returns : string
Args : string
=cut
sub executable {
my ($self, $exe) = @_;
if ($exe)
{
$self->{'_exe'} = $exe;
}
return $self->{'_exe'};
}
=head2 library
Title : library
Usage : $self->library('sw');
Function: Get/set for a library to search in - eg efetch wil not search swall without the prefix sw:
Returns : string
Args : string
=cut
sub library {
my ($self, $lib) = @_;
if ($lib) {
$self->{'_lib'} = $lib;
}
return $self->{'_lib'};
}
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $self->get_Seq_by_acc($accession);
Function: Does the sequence retrieval via efetch
Returns : Bio::Seq
Args :
=cut
sub get_Seq_by_acc {
my ($self, $acc) = @_;
if (!defined($acc)) {
$self->throw("No accession input");
}
my $lib = $self->library;
if (defined $lib && $lib ne ''){
$acc = $lib . ":" . $acc;
}
my $seqstr;
my $seq;
my $efetch = $self->executable;
open(IN,"$efetch -q $acc |") or $self->throw("Error running efetch for acc [$acc]: $efetch");
$seqstr = <IN>;
close IN;
if(defined $seqstr && $seqstr ne "no match") {
chomp($seqstr);
$seq = new Bio::Seq('-seq' => $seqstr,
'-accession_number' => $acc,
'-display_id' => $acc);
}
$self->throw("Could not efetch sequence for [$acc]\n") unless defined $seq;
return $seq;
}
1;
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