Raw content of Bio::EnsEMBL::Pipeline::SeqFetcher::BioIndex
<![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::BioIndex
=head1 SYNOPSIS
my $obj = Bio::EnsEMBL::Pipeline::SeqFetcher::BioIndex->new(
-db => $db
);
my $seq = $obj->get_Seq_by_acc($acc);
=head1 DESCRIPTION
Object to retrieve sequences as Bio::Seq, using getseqs by James Cuff. Sequences are fetched from a
database previously formatted with makeindex
=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::BioIndex;
use strict;
use Bio::EnsEMBL::Root;
use Bio::EnsEMBL::Pipeline::SeqFetcher::DBIndex;
use Bio::Seq;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Root);
sub new {
my ($class, @args) = @_;
my $self = bless {}, $class;
my ($db) = $self->_rearrange(['DB'], @args);
# expect an array of dbs
$self->throw("Expected a reference to an array of db [" . ref($db) . "]\n") unless ref($db) eq 'ARRAY';
if (defined $db) {
$self->db($db);
}
return $self; # success - we hope!
}
=head2 db
Title : db
Usage : $self->db('/data/blastdb/dbname');
Function: Get/set for dbs to be searched. Checks that the database
appropriate files are present, but nothing else.
Returns : string
Args : string
=cut
sub db {
my ($self, $dbs) = @_;
if (!defined($self->{'_db'})) {
$self->{'_db'} = [];
}
if (defined $dbs){
if (ref($dbs) eq 'ARRAY') {
foreach my $db(@$dbs){
$self->throw("are you sure that $db has been formatted with DBIndex? Some files are missing\n")
unless (-d "$db" && -e "$db/config.dat" && -e "$db/fileids.dat");
my $index = new Bio::EnsEMBL::Pipeline::SeqFetcher::DBIndex(-database => $db);
$self->index($index);
push (@{$self->{'_db'}},$db);
}
}
}
return (@{$self->{'_db'}});
}
=head2 index
Title : index
Usage : Get/set function for storing the Bio indexes
Function: Is only called internally to tthe object
Example : $seqfetcher->index
Returns : array of Bio::EnsEMBL::Pipeline::SeqFetcher::Index
Args : nothing or Bio::EnsEMBL::Pipeline::SeqFetcher::Index
=cut
sub index {
my ($self,$arg) = @_;
if (!defined ($self->{_index})) {
$self->{_index} = [];
}
if (defined($arg)) {
push(@{$self->{_index}},$arg);
}
return @{$self->{_index}};
}
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $self->get_Seq_by_acc($accession);
Function: Does the sequence retrieval via getseqs
Returns : Bio::Seq
Args :
=cut
sub get_Seq_by_acc {
my ($self, $acc) = @_;
if (!defined($acc)) {
$self->throw("No accession input");
}
my $seq;
foreach my $index ($self->index) {
my $entry = $index->get_Seq_by_id($acc);
if ($entry ne "") {
print "Entry\n";
my ($idstr,$seqstr) = split(/\n/,$entry,2);
my ($id,$desc) = split(/ /,$idstr,2);
$id =~ s/^>//;
$seqstr =~ s/\n//g;
my $seq = new Bio::Seq(-id => $acc,
-display_id => $acc,
-seq => $seqstr);
return $seq;
}
}
return;
}
sub get_Seq_by_id {
my $self = @_;
return undef;
}
1;
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