Raw content of Bio::DB::XEMBL
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# $Id: XEMBL.pm,v 1.3 2002/10/22 07:38:29 lapp Exp $
#
# BioPerl module for Bio::DB::XEMBL
#
# Cared for by Lincoln Stein
#
# Copyright Lincoln Stein
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::XEMBL - Database object interface for XEMBL entry retrieval
=head1 SYNOPSIS
use Bio::DB::XEMBL;
$embl = new Bio::DB::XEMBL;
# remember that XEMBL_ID does not equal GenBank_ID!
$seq = $embl->get_Seq_by_id('BUM'); # EMBL ID
print "cloneid is ", $seq->id, "\n";
# or changeing to accession number and Fasta format ...
$seq = $embl->get_Seq_by_acc('J02231'); # XEMBL ACC
print "cloneid is ", $seq->id, "\n";
# especially when using versions, you better be prepared
# in not getting what what want
eval {
$seq = $embl->get_Seq_by_version('J02231.1'); # XEMBL VERSION
}
print "cloneid is ", $seq->id, "\n" unless $@;
my $seqio = $embl->get_Stream_by_batch(['U83300','U83301','U83302']);
while( my $clone = $seqio->next_seq ) {
print "cloneid is ", $clone->id, "\n";
}
=head1 DESCRIPTION
Allows the dynamic retrieval of Bio::Seq objects from the XEMBL
database. See L<Bio::Seq> for details.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Lincoln Stein
Email Lincoln Stein E<lt>lstein@cshl.orgE<gt>
=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::DB::XEMBL;
use strict;
use Bio::DB::RandomAccessI;
use Bio::DB::XEMBLService 'getNucSeq';
# bsml parser appears broken...
use Bio::SeqIO::bsml;
use File::Temp 'tempfile';
use vars qw(@ISA $MODVERSION);
@ISA = qw(Bio::DB::RandomAccessI);
$MODVERSION = '0.1';
sub new {
my ($class, @args ) = @_;
my $self = $class->SUPER::new(@args);
return $self;
}
=head2 get_Seq_by_id
Title : get_Seq_by_id
Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
Function: Gets a Bio::Seq object by its name
Returns : a Bio::Seq object
Args : the id (as a string) of a sequence
Throws : "id does not exist" exception
=cut
sub get_Seq_by_id {
my ($self,@args) = @_;
my $seqio = $self->get_Stream_by_batch([@args]);
return $seqio->next_seq;
}
=head2 get_Stream_by_batch
Title : get_Stream_by_batch
Usage : $seq = $db->get_Stream_by_batch($ref);
Function: Retrieves Seq objects from XEMBL 'en masse', rather than one
at a time. Currently this is not particularly efficient, as
it loads the entire result into memory and parses it.
Example :
Returns : a Bio::SeqIO stream object
Args : $ref : an array reference containing a list of unique
ids/accession numbers.
=cut
sub get_Stream_by_batch {
my ($self, $ids) = @_;
$self->throw("expected an array ref, but got $ids")
unless ref($ids) eq 'ARRAY';
my @args = @$ids;
my $result = getNucSeq(SOAP::Data->name(format=>'bsml'),
SOAP::Data->name(ids=>"@args"))
or $self->throw('id does not exist');
my($fh,$filename) = tempfile(File::Spec->tmpdir . '/bsmlXXXXXX',SUFFIX=>'.bsml');
print $fh $result;
close $fh;
my $seqio = Bio::SeqIO->new(-file=>$filename,-format=>'bsml');
unlink $filename;
$seqio;
}
*get_Stream_by_id = \&get_Stream_by_batch;
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc('X77802');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object
Args : accession number (as a string)
Throws : "acc does not exist" exception
=cut
sub get_Seq_by_acc{
my ($self,@args) = @_;
return $self->get_Seq_by_id(@args);
}
=head2 get_Seq_by_version
Title : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_version('X77802.1');
Function: Gets a Bio::Seq object by sequence version
Returns : A Bio::Seq object
Args : accession.version (as a string)
Throws : "acc.version does not exist" exception
=cut
sub get_Seq_by_version{
my ($self,@args) = @_;
return $self->get_Seq_by_id(@args);
}
1;
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