diff variant_effect_predictor/Bio/DB/XEMBL.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/DB/XEMBL.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,184 @@
+#
+# $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.
+
+  [e-mail]                         - 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:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Lincoln Stein
+
+Email Lincoln Stein E<lt>[e-mail]<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;