Raw content of Bio::EnsEMBL::Pipeline::SeqFetcher::BPIndex
<![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::BPIndex
=head1 SYNOPSIS
my $obj = Bio::EnsEMBL::Pipeline::SeqFetcher::BPIndex->new(
'-index' => $index,
'-format' => 'Fasta',
);
my $seq = $obj->get_Seq_by_acc($acc);
=head1 DESCRIPTION
Object to retrieve sequences as Bio::Seq, from a bioperl index.
The index is not made by this module; instead, the absolute path
to the bioperl index must be set using $obj->bp_index. The format
of the database must be set using bp_format.
=head1 CONTACT
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::EnsEMBL::Pipeline::SeqFetcher::BPIndex;
use strict;
use Bio::EnsEMBL::Root;
use Bio::DB::RandomAccessI;
use Bio::Seq;
# change these uses as new indices are released in bioperl - these are for 0.6.2
use Bio::Index::Fasta;
use Bio::Index::EMBL;
use Bio::Index::SwissPfam;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Root Bio::DB::RandomAccessI);
sub new {
my ($class, @args) = @_;
my $self = bless {}, $class;
my($index, $format) = $self->_rearrange(['INDEX',
'FORMAT'], @args);
if (!defined $index) {
$self->throw("No bioperl indexfile provided to BPIndex\n");
}
$self->bp_index($index);
if (!defined $format) {
$self->throw("No bioperl index format provided to BPIndex\n");
}
$self->bp_format($format);
return $self; # success - we hope!
}
=head2 bp_index
Title : bp_index
Usage : $self->bp_index('/usr/local/ensembl/data/bp.inx')
Function: Get/set for a bioperl index
Returns : path to bioperl index
Args : path to bioperl index
=cut
sub bp_index {
my ($self, $inx) = @_;
if ($inx)
{
$self->{'_inx'} = $inx;
}
return $self->{'_inx'};
}
=head2 bp_format
Title : bp_format
Usage : $self->bp_format('Fasta')
Function: Get/set for a bioperl index format
Returns : String representing format. NOTE - bp_format is used in run to identify the type of Bio::Index module to make - so case is crucial. eg Fasta, EMBL, SwissPfam
Args : String representing format
=cut
sub bp_format {
my ($self, $format) = @_;
if ($format)
{
$self->{'_format'} = $format;
}
return $self->{'_format'};
}
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $self->get_Seq_by_acc($accession);
Function: Does the sequence retrieval
Returns : Bio::Seq
Args :
=cut
sub get_Seq_by_acc {
my ($self, $acc) = @_;
my $inx = $self->bp_index;
my $format = $self->bp_format;
if (!defined($acc)) {
$self->throw("No accession input");
}
if (!defined($inx)) {
$self->throw("No search index specified; cannot run");
}
if (!defined($format)) {
$self->throw("No index format specified");
}
my $type = 'Bio::Index::' . $format;
my $index;
eval {
$index = $type->new($inx);
};
if ($@) {
my $tmp = $@; # for some reason, warn empties out $@ ...
$self->warn("Problem opening the index [$inx] - check you have supplied the right format!");
$self->throw ("[$tmp]!");
}
# get the sequence
my $seq;
eval{
$seq = $index->fetch($acc); # Returns Bio::Seq object
};
$self->throw("Could not fetch sequence for [$acc]") unless defined $seq;
return $seq;
}
1;
]]>