Raw content of Bio::EnsEMBL::Pipeline::SeqFetcher::xdget
<![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::xdget
=head1 SYNOPSIS
my $obj = Bio::EnsEMBL::Pipeline::SeqFetcher::xdget->new(
-executable => '/blah/xdget',
-db => '/data/db'
);
my $seq = $obj->get_Seq_by_acc($acc);
=head1 DESCRIPTION
Object to retrieve sequences using xdget (Wash U).
Database must be formatted with xdformat. Sequence type (protein
or nucleotide) is guessed, based on file extensions of the database
files. Returns sequence as Bio::Seq.
Additional options for xdget can be specifed though no checking
is performed for compatibility.
Note that, at the time of writing, xdget is case-insensitive:
retrieved sequence is in upper case, irrespective of what was
in the original unformatted fasta file.
=head1 CONTACT
B<ensembl-dev@ebi.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Pipeline::SeqFetcher::xdget;
use strict;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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, $options, $db) = rearrange([qw(
EXECUTABLE OPTIONS DB
)], @args);
$exe ||= 'xdget';
$self->executable($exe);
$self->options($options) if defined $options;
$self->db($db) if defined $db;
return $self;
}
=head2 executable
Title : executable
Usage : $self->executable('/path/to/executable');
Function: Get/set for the executable to be used by the module.
Returns : string
Args : string
=cut
sub executable {
my ($self, $exe) = @_;
if ($exe) {
$self->{'_exe'} = $exe;
}
return $self->{'_exe'};
}
=head2 db
Title : db
Usage : $self->db('/path/to/db');
Function: Get/set for the db to be used by the module.
Returns : string
Args : string
=cut
sub db {
my ($self, $dbref) = @_;
if ($dbref) {
foreach my $db (@$dbref) {
my @f = glob "$db.x??";
my @p = grep (/\.xp./,@f);
my @n = grep (/\.xn./,@f);
if (@p) {
$self->_moltype($db, 'p');
} elsif (@n) {
$self->_moltype($db, 'n');
} else {
throw("XDF database $db appears to be missing files");
}
push @{$self->{'_db'}}, $db;
}
}
return $self->{'_db'};
}
=head2 options
Title : options
Usage : $self->options('-r');
Returns reverse complement of nucleotide sequence
Function: Get/set for options to xdget
Returns : string
Args : string
=cut
sub options {
my ($self, $options) = @_;
if ($options) {
$self->{'_options'} = $options;
}
return $self->{'_options'};
}
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $self->get_eq_by_acc($accession);
Function: retrieves sequence via xdget
Returns : Bio::Seq
Args : Sequence identifier string
=cut
sub get_Seq_by_acc {
my ($self, $acc) = @_;
throw("No accession input") unless $acc;
throw("No database defined") unless $self->db;
my $xdget = $self->executable;
my $db = $self->db;
local *FH;
my $seq;
my $seqstr;
my $desc;
my $command;
my @out;
# maybe should have some checking here to see if -n/-p have
# already been specified in options
DB: foreach my $db (@{$self->db}) {
my $options = $self->options;
if ($self->_moltype($db) eq 'n') {
$options .= " -n";
}
else {
$options .= " -p";
}
$command = "$xdget $options $db $acc";
open FH, "$command 2>&1 |" or throw("Error retrieving $acc from $db with $xdget");
@out = <FH>;
close FH;
last DB if $out[0] !~ /Not found/;
}
$desc = shift @out;
$seqstr = join(" ", @out);
$desc =~ s/^>//;chomp $desc;
$seqstr =~ s/\s//g;
$seq = Bio::Seq->new(
-seq => $seqstr,
-display_id => $acc,
-accession_number => $acc,
-desc => $desc
);
return $seq;
}
sub _moltype {
my ($self, $db, $type) = @_;
return undef unless $db;
if ($type) {
$self->{'_moltype'}{$db} = $type;
}
return $self->{'_moltype'}{$db};
}
1;
]]>