Raw content of Bio::EnsEMBL::Pipeline::SeqFetcher::Getz
<![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::Getz
=head1 SYNOPSIS
my $obj = Bio::EnsEMBL::Pipeline::SeqFetcher::Getz->new(
'-executable' => $exe,
'-library' => $lib,
);
my $seq = $obj->get_Seq_by_acc($acc);
=head1 DESCRIPTION
Object to retrieve sequences as Bio::Seq, using getz.
=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::Getz;
use strict;
use Bio::EnsEMBL::Root;
use Bio::DB::RandomAccessI;
use Bio::Seq;
use Bio::SeqIO;
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 = 'getz';
}
$self->executable($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 : $self->library('embl');
Function: Get/set for a library/libraries to search in
Returns : string
Args : string
=cut
sub library {
my ($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 getz
Returns : Bio::Seq
Args :
=cut
sub get_Seq_by_acc {
my ($self, $acc) = @_;
my $libs = $self->library;
if (!defined($acc)) {
$self->throw("No id input");
}
if (!defined($libs)) {
$self->throw("No search libs specified");
}
my $seqstr;
my $seq;
my $getz = $self->executable;
open(IN, "$getz -d -sf fasta '[libs={$libs}-AccNumber:$acc]' |")
or $self->throw("Error running getz for id [$acc]: $getz");
my $format = 'fasta';
my $fh = Bio::SeqIO->new(-fh => \*IN, "-format"=>$format);
$seq = $fh->next_seq();
close IN;
$self->throw("Could not getz sequence for [$acc]\n") unless defined $seq;
$seq->display_id($acc);
$seq->accession_number($acc);
return $seq;
}
=head2 get_Seq_by_id
Title : get_Seq_by_id
Usage : $self->get_Seq_by_id($id);
Function: Does the sequence retrieval via getz
Returns : Bio::Seq
Args :
=cut
sub get_Seq_by_id {
my ($self, $id) = @_;
my $libs = $self->library;
if (!defined($id)) {
$self->throw("No id input");
}
if (!defined($libs)) {
$self->throw("No search libs specified");
}
my $seqstr;
my $seq;
my $getz = $self->executable;
open(IN, "$getz -d -sf fasta '[libs={$libs}-ID:$id]' |")
or $self->throw("Error running getz for id [$id]: $getz");
my $format = 'fasta';
my $fh = Bio::SeqIO->new(-fh => \*IN, "-format"=>$format);
$seq = $fh->next_seq();
close IN;
$self->throw("Could not getz sequence for [$id]\n") unless defined $seq;
$seq->display_id($id);
$seq->accession_number($id);
return $seq;
}
=head2 batch_fetch
Title : batch_fetch
Usage : $self->batch_fetch(@accs);
Function: Retrieves batches of sequences
Returns : listref of Bio::Seq
Args :
=cut
# This method is not yet couth. getz can retrieve multiple sequences at
# once - this method should be reimplemented to do things this way, rather
# than this five-for-the-price-of-five approach.
sub batch_fetch {
my ($self, @accs) = @_;
my @seqs;
while (@accs){
push @seqs, $self->get_Seq_by_acc(shift @accs);
}
return \@seqs
}
1;
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