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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/DB/EMBL.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,209 @@
+#
+# $Id: EMBL.pm,v 1.12.2.1 2003/06/25 13:44:18 heikki 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::EMBL - Database object interface for EMBL entry retrieval
+
+=head1 SYNOPSIS
+
+  use Bio::DB::EMBL;
+
+  $embl = new Bio::DB::EMBL;
+
+  # remember that EMBL_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 ...
+  $embl->request_format('fasta');
+  $seq = $embl->get_Seq_by_acc('J02231'); # EMBL 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'); # EMBL VERSION
+  };
+  print "cloneid is ", $seq->id, "\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
+  $embl = new Bio::DB::EMBL(-retrievaltype => 'tempfile' ,
+ 			    -format => 'fasta');
+  my $seqio = $embl->get_Stream_by_batch(['AC013798', 'AC021953'] );
+  while( my $clone =  $seqio->next_seq ) {
+ 	print "cloneid is ", $clone->id, "\n";
+  }
+
+=head1 DESCRIPTION
+
+Allows the dynamic retrieval of sequence objects L<Bio::Seq> from the
+EMBL database using the dbfetch script at EBI:
+L<http://www.ebi.ac.uk/cgi-bin/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>.
+
+=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::EMBL;
+use strict;
+use vars qw(@ISA $MODVERSION %HOSTS  %FORMATMAP  $DEFAULTFORMAT);
+
+$MODVERSION = '0.2';
+use Bio::DB::DBFetch;
+use Bio::DB::RefSeq;
+
+@ISA = qw(Bio::DB::DBFetch);
+
+BEGIN {
+    # you can add your own here theoretically.
+    %HOSTS = (
+	       'dbfetch' => {
+		   baseurl => 'http://%s/cgi-bin/dbfetch?db=embl&style=raw',
+		   hosts   => {
+		       'ebi'  => 'www.ebi.ac.uk'
+		       }
+	       }
+	      );
+    %FORMATMAP = ( 'embl' => 'embl',
+		   'fasta' => 'fasta'
+		   );
+    $DEFAULTFORMAT = 'embl';
+}
+
+=head2 new
+
+ Title   : new
+ Usage   : $gb = Bio::DB::GenBank->new(@options)
+ Function: Creates a new genbank handle
+ Returns : New genbank handle
+ Args    : -delay   number of seconds to delay between fetches (3s)
+
+NOTE:  There are other options that are used internally.
+
+=cut
+
+sub new {
+    my ($class, @args ) = @_;
+    my $self = $class->SUPER::new(@args);
+
+    $self->{ '_hosts' } = {};
+    $self->{ '_formatmap' } = {};
+
+    $self->hosts(\%HOSTS);
+    $self->formatmap(\%FORMATMAP);
+    $self->{'_default_format'} = $DEFAULTFORMAT;
+
+    return $self;
+}
+
+
+=head2 Bio::DB::WebDBSeqI methods
+
+Overriding WebDBSeqI method to help newbies to retrieve sequences.
+EMBL database is all too often passed RefSeq accessions. This
+redirects those calls. See L<Bio::DB::RefSeq>.
+
+
+=head2 get_Stream_by_acc
+
+  Title   : get_Stream_by_acc
+  Usage   : $seq = $db->get_Seq_by_acc([$acc1, $acc2]);
+  Function: Gets a series of Seq objects by accession numbers
+  Returns : a Bio::SeqIO stream object
+  Args    : $ref : a reference to an array of accession numbers for
+                   the desired sequence entries
+  Note    : For GenBank, this just calls the same code for get_Stream_by_id()
+
+=cut
+
+sub get_Stream_by_acc {
+    my ($self, $ids ) = @_;
+    my $newdb = $self->_check_id($ids);
+    if ($newdb && $newdb->isa('Bio::DB::RefSeq')) {
+	return $newdb->get_seq_stream('-uids' => $ids, '-mode' => 'single');
+    } else {
+	return $self->get_seq_stream('-uids' => $ids, '-mode' => 'single');
+    }
+}
+
+
+=head2 _check_id
+
+  Title   : _check_id
+  Usage   : 
+  Function: 
+  Returns : A Bio::DB::RefSeq reference or throws
+  Args    : $id(s), $string
+=cut
+
+sub _check_id {
+    my ($self, $ids) = @_;
+
+    # NT contigs can not be retrieved
+    $self->throw("NT_ contigs are whole chromosome files which are not part of regular".
+		 "database distributions. Go to ftp://ftp.ncbi.nih.gov/genomes/.") 
+	if $ids =~ /NT_/;
+
+    # Asking for a RefSeq from EMBL/GenBank
+
+    if ($ids =~ /N._/) {
+	$self->warn("[$ids] is not a normal sequence database but a RefSeq entry.".
+		   " Redirecting the request.\n")
+	    if $self->verbose >= 0;
+	return  new Bio::DB::RefSeq(-verbose => $self->verbose);
+    }
+}
+
+
+1;