diff variant_effect_predictor/Bio/DB/Flat/BDB/embl.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/DB/Flat/BDB/embl.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,97 @@
+#
+# $Id: embl.pm,v 1.4 2002/10/22 07:38:31 lapp Exp $
+#
+# BioPerl module for Bio::DB::Flat::BDB
+#
+# Cared for by Lincoln Stein <[e-mail]>
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::DB::Flat::BDB::embl - embl adaptor for Open-bio standard BDB-indexed flat file
+
+=head1 SYNOPSIS
+
+See Bio::DB::Flat.
+
+=head1 DESCRIPTION
+
+This module allows embl files to be stored in Berkeley DB flat files
+using the Open-Bio standard BDB-indexed flat file scheme.  You should
+not be using this directly, but instead use it via Bio::DB::Flat.
+
+=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://bioperl.org/MailList.shtml - 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 - [e-mail]
+
+=head1 SEE ALSO
+
+L<Bio::DB::Flat>,
+
+=cut
+
+package Bio::DB::Flat::BDB::embl;
+
+use strict;
+use Bio::DB::Flat::BDB;
+use vars '@ISA';
+
+@ISA = qw(Bio::DB::Flat::BDB);
+
+sub parse_one_record {
+  my $self  = shift;
+  my $fh    = shift;
+  my $parser =
+    $self->{embl_cached_parsers}{fileno($fh)} ||= Bio::SeqIO->new(-fh=>$fh,-format=>$self->default_file_format);
+  my $seq = $parser->next_seq;
+  my $ids = $self->seq_to_ids($seq);
+  return $ids;
+}
+
+sub seq_to_ids {
+  my $self = shift;
+  my $seq  = shift;
+
+  my $display_id = $seq->display_id;
+  my $accession  = $seq->accession_number;
+  my %ids;
+  $ids{ID}       = $display_id;
+  $ids{ACC}      = $accession   if defined $accession;
+  return \%ids;
+}
+
+sub default_primary_namespace {
+  return "ID";
+}
+
+sub default_secondary_namespaces {
+  return qw(ACC);
+}
+
+sub default_file_format { "embl" }
+
+
+1;