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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Index/EMBL.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,213 @@
+# $Id: EMBL.pm,v 1.21.2.1 2003/03/19 16:23:08 heikki Exp $
+#
+# BioPerl module for Bio::Index::EMBL
+#
+# Cared for by Ewan Birney <[e-mail]>
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot
+.dat files (ie flat file embl/swissprot format).
+
+=head1 SYNOPSIS
+
+    # Complete code for making an index for several
+    # EMBL files
+    use Bio::Index::EMBL;
+    use strict;
+
+    my $Index_File_Name = shift;
+    my $inx = Bio::Index::EMBL->new('-filename' => $Index_File_Name,
+				    '-write_flag' => 'WRITE');
+    $inx->make_index(@ARGV);
+
+    # Print out several sequences present in the index
+    # in Fasta format
+    use Bio::Index::EMBL;
+    use strict;
+
+    my $Index_File_Name = shift;
+    my $inx = Bio::Index::EMBL->new('-filename' => $Index_File_Name);
+    my $out = Bio::SeqIO->new('-format' => 'Fasta','-fh' => \*STDOUT);
+
+    foreach my $id (@ARGV) {
+        my $seq = $inx->fetch($id); # Returns Bio::Seq object
+	$out->write_seq($seq);
+    }
+
+    # alternatively
+
+    my $seq1 = $inx->get_Seq_by_id($id);
+    my $seq2 = $inx->get_Seq_by_acc($acc);
+
+=head1 DESCRIPTION
+
+Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
+and provides the basic funtionallity for indexing EMBL files, and
+retrieving the sequence from them. Heavily snaffled from James Gilbert's
+Fasta system. Note: for best results 'use strict'.
+
+=head1 FEED_BACK
+
+=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 - Ewan Birney
+
+Email - [e-mail]
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let's begin the code...
+
+
+package Bio::Index::EMBL;
+
+use vars qw($VERSION @ISA);
+use strict;
+
+use Bio::Index::AbstractSeq;
+use Bio::Seq;
+
+@ISA = qw(Bio::Index::AbstractSeq);
+
+sub _type_stamp {
+    return '__EMBL_FLAT__'; # What kind of index are we?
+}
+
+#
+# Suggested fix by Michael G Schwern <[e-mail]> to
+# get around a clash with CPAN shell...
+#
+
+BEGIN {
+    $VERSION = 0.1;
+}
+
+sub _version {
+    return $VERSION;
+}
+
+=head2 _index_file
+
+  Title   : _index_file
+  Usage   : $index->_index_file( $file_name, $i )
+  Function: Specialist function to index EMBL format files.
+            Is provided with a filename and an integer
+            by make_index in its SUPER class.
+  Example : 
+  Returns : 
+  Args    : 
+
+=cut
+
+sub _index_file {
+    my( $self,
+        $file, # File name
+        $i     # Index-number of file being indexed
+        ) = @_;
+
+    my( $begin, # Offset from start of file of the start
+                # of the last found record.
+        $id,    # ID of last found record.
+	@accs,   # accession of last record. Also put into the index
+        );
+
+    $begin = 0;
+
+    open EMBL, $file or $self->throw("Can't open file for read : $file");
+
+    # Main indexing loop
+    $id = undef;
+    @accs = ();
+    while (<EMBL>) {
+	if( /^\/\// ) {
+	    if( ! defined $id ) {
+		$self->throw("Got to a end of entry line for an EMBL flat file with no parsed ID. Considering this a problem!");
+		next;
+	    }
+	    if( ! @accs ) {
+		$self->warn("For id [$id] in embl flat file, got no accession number. Storing id index anyway");
+	    }
+
+	    $self->add_record($id, $i, $begin);
+
+	    foreach my $acc (@accs) {
+		if( $acc ne $id ) {
+		    $self->add_record($acc, $i, $begin);
+		}
+	    }
+	} elsif (/^ID\s+(\S+)/) {
+	    $id = $1;
+	    # not sure if I like this. Assummes tell is in bytes.
+	    # we could tell before each line and save it.
+            $begin = tell(EMBL) - length( $_ );
+	
+	} elsif (/^AC\s+(.*)?/) {
+            push @accs , split (/[; ]+/, $1);
+	} else {
+	    # do nothing
+	}
+    }
+
+    close EMBL;
+    return 1;
+}
+
+=head2 _file_format
+
+ Title   : _file_format
+ Usage   : Internal function for indexing system
+ Function: Provides file format for this database
+ Example :
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub _file_format{
+   my ($self,@args) = @_;
+
+   return 'EMBL';
+}
+
+
+
+1;
+
+
+
+
+
+
+
+
+
+