Raw content of Bio::EnsEMBL::Pipeline::SeqFetcher::FileIndex
<![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::Pfetch
=head1 SYNOPSIS
my $obj = Bio::EnsEMBL::Pipeline::SeqFetcher::Pfetch->new(
-executable => $exe
);
my $seq = $obj->get_Seq_by_acc($acc);
=head1 DESCRIPTION
Object to retrieve sequences as Bio::Seq, using pfetch.
=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::FileIndex;
use strict;
use Bio::EnsEMBL::Root;
use Bio::DB::RandomAccessI;
use Bio::SeqIO;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Root Bio::DB::RandomAccessI);
sub new {
my ($class, @args) = @_;
my $self = bless {}, $class;
my ($seqfile) = $self->_rearrange(['SEQFILE'], @args);
if (defined($seqfile)) {
$self->seqfile($seqfile);
} else {
$self->throw("Need a sequence file");
}
return $self; # success - we hope!
}
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $self->get_eq_by_acc($accession);
Function: Does the sequence retrieval
Returns : Bio::Seq
Args :
=cut
sub get_Seq_by_acc {
my ($self, $acc) = @_;
if (!defined($acc)) {
$self->throw("No accession input");
}
if (defined($self->{_seqhash}{$acc})) {
return $self->{_seqhash}{$acc};
} else {
$self->throw("Could not fetch sequence for [$acc]\n");
}
}
sub seqfile {
my ($self,$file) = @_;
if (defined($file)) {
open (INDEX,"<$file") || $self->throw("Can't open $file");
my $seqio = new Bio::SeqIO(-fh => \*INDEX, -format => 'fasta');
while (my $seq = $seqio->next_seq) {
$self->{_seqhash}{$seq->id} = $seq;
}
close(INDEX);
} else {
$self->throw("Must supply a seqfile to Bio:EnsEMBL::Pipeline::SeqFetcher::FileIndex");
}
}
sub list_all_ids {
my ($self) = @_;
my @ids = keys %{$self->{_seqhash}};
return \@ids;
}
1;
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