Raw content of Bio::EnsEMBL::Pipeline::SeqFetcher::Getseqs
<![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::Getseqs
=head1 SYNOPSIS
my $obj = Bio::EnsEMBL::Pipeline::SeqFetcher::Getseqs->new(
-executable => $exe,
-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::Getseqs;
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, $db) = $self->_rearrange(['EXECUTABLE', 'DB'], @args);
if (!defined $exe) {
$exe = 'getseqs';
}
$self->executable($exe);
# expect an array of dbs
$self->throw("Expected a reference to an array of db\n") unless ref($db) eq 'ARRAY';
if (defined $db) {
$self->db($db);
}
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 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 $db has been formatted with makeindex?\n")
unless ( -e "$db.jidx");
push (@{$self->{'_db'}},$db);
}
}
}
return (@{$self->{'_db'}});
}
=head2 get_Seq_byacc
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 $seqstr;
my $seq;
my $getseqs = $self->executable;
my @seqdb = $self->db;
SEQDB:
while(scalar(@seqdb) && !(defined $seq)){
my $database = pop(@seqdb);
last SEQDB unless defined $database;
my $cmd = "$getseqs '$acc' $database";
open(IN,"$cmd 2>/dev/null |") or $self->throw("Error forking getseqs for accession [$acc]: getseqs");
my $seqstr;
while(<IN>){
chomp;
$seqstr .= $_;
}
close IN or $self->throw("Error running getseqs for $acc: $!\n");
if(defined $seqstr && !($seqstr=~/Sorry/)) {
chomp($seqstr);
$seq = new Bio::Seq('-seq' => $seqstr,
'-accession_number' => $acc,
'-desc' => "",
'-display_id' => $acc);
}
}
$self->throw("Could not getseqs sequence for [$acc]\n") unless defined $seq;
return $seq;
}
sub get_Seq_by_id {
my $self = @_;
return undef;
}
1;
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