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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/DB/RefSeq.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,142 @@
+#
+# $Id: RefSeq.pm,v 1.5 2002/10/22 07:38:29 lapp Exp $
+#
+# BioPerl module for Bio::DB::EMBL
+#
+# Cared for by Heikki Lehvaslaiho <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::DB::RefSeq - Database object interface for RefSeq retrieval
+
+=head1 SYNOPSIS
+  use Bio::DB::RefSeq;
+
+  $db = new Bio::DB::RefSeq;
+
+  # most of the time RefSeq_ID eq RefSeq acc
+  $seq = $db->get_Seq_by_id('NM_006732'); # RefSeq ID
+  print "accession is ", $seq->accession_number, "\n";
+
+  # or changeing to accession number and Fasta format ...
+  $db->request_format('fasta');
+  $seq = $db->get_Seq_by_acc('NM_006732'); # RefSeq ACC
+  print "seq is ", $seq->seq, "\n";
+
+  # especially when using versions, you better be prepared
+  # in not getting what what want
+  eval {
+      $seq = $db->get_Seq_by_version('NM_006732.1'); # RefSeq VERSION
+  };
+  print "accesion is ", $seq->accession_number, "\n" unless $@;
+
+  # or ... best when downloading very large files, prevents
+  # keeping all of the file in memory
+
+  # also don't want features, just sequence so let's save bandwith
+  # and request Fasta sequence
+  $db = new Bio::DB::RefSeq(-retrievaltype => 'tempfile' ,
+ 			       -format => 'fasta');
+  my $seqio = $db->get_Stream_by_batch(['NM_006732', 'NM_005252'] );
+  while( my $seq  =  $seqio->next_seq ) {
+ 	print "seqid is ", $seq->id, "\n";
+  }
+
+=head1 DESCRIPTION
+
+Allows the dynamic retrieval of sequence objects L<Bio::Seq> from the
+RefSeq database using the dbfetch script at EBI:
+L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>cgi-binE<sol>dbfetch>.
+
+In order to make changes transparent we have host type (currently only
+ebi) and location (defaults to ebi) separated out.  This allows later
+additions of more servers in different geographical locations.
+
+The functionality of this module is inherited from L<Bio::DB::DBFetch>
+which implements L<Bio::DB::WebDBSeqI>.
+
+This module retrieves entries from EBI although it
+retrives database entries produced at NCBI. When read into bioperl
+objects, the parser for GenBank format it used. RefSeq is a
+NONSTANDARD GenBank file so be ready for surprises.
+
+=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 - Heikki Lehvaslaiho
+
+Email Heikki Lehvaslaiho 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::RefSeq;
+use strict;
+use vars qw(@ISA $MODVERSION %HOSTS  %FORMATMAP $DEFAULTFORMAT);
+
+$MODVERSION = '0.1';
+use Bio::DB::DBFetch;
+
+@ISA = qw(Bio::DB::DBFetch);
+
+BEGIN {
+    # you can add your own here theoretically.
+    %HOSTS = (
+	       'dbfetch' => {
+		   baseurl => 'http://%s/cgi-bin/dbfetch?db=refseq&style=raw',
+		   hosts   => {
+		       'ebi'  => 'www.ebi.ac.uk'
+		       }
+	       }
+	      );
+    %FORMATMAP = ( 'embl'    => 'embl',
+		   'genbank' => 'genbank',
+		   'fasta' => 'fasta'
+		   );
+    $DEFAULTFORMAT = 'genbank';
+}
+
+sub new {
+    my ($class, @args ) = @_;
+    my $self = $class->SUPER::new(@args);
+
+    $self->{ '_hosts' } = {};
+    $self->{ '_formatmap' } = {};
+
+    $self->hosts(\%HOSTS);
+    $self->formatmap(\%FORMATMAP);
+    $self->{'_default_format'} = $DEFAULTFORMAT;
+
+    return $self;
+}
+
+1;