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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Index/SwissPfam.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,206 @@
+
+#
+# $Id: SwissPfam.pm,v 1.15 2002/10/22 07:38:33 lapp Exp $
+#
+# BioPerl module for Bio::Index::SwissPfam
+#
+# 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::SwissPfam - Interface for indexing swisspfam files
+
+=head1 SYNOPSIS
+
+    use Bio::Index::SwissPfam;
+    use strict;
+
+    my $Index_File_Name = shift;
+    my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name, 
+					 '-write_flag' => 'WRITE');
+    $inx->make_index(@ARGV);
+
+    use Bio::Index::SwissPfam;
+    use strict;
+
+    my $Index_File_Name = shift;
+    my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name);
+
+    foreach my $id (@ARGV) {
+        my $seq = $inx->fetch($id); # Returns stream
+	while( <$seq> ) {
+	    if(/^>/) {
+	    	print;
+		last;
+	    }
+	}
+    }
+
+
+=head1 DESCRIPTION
+
+SwissPfam is one of the flat files released with Pfam. This modules
+provides a way of indexing this module.
+
+Inherits functions for managing dbm files from
+Bio::Index::Abstract.pm, and provides the basic funtionallity for
+indexing SwissPfam files.  Only retrieves FileStreams at the
+moment. Once we have something better (ie, an object!), will use
+that. Heavily snaffled from James Gilbert's Fasta system. Note: for
+best results 'use strict'.
+
+=head1 FEED_BACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to one
+of the Bioperl mailing lists.  Your participation is much appreciated.
+
+  [e-mail]             - General discussion
+  http://bioperl.org/MailList.shtml - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+the bugs and their resolution.  Bug reports can be submitted via
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Ewan Birney
+
+Email - [e-mail]
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let's begin the code...
+
+
+package Bio::Index::SwissPfam;
+
+use vars qw($VERSION @ISA);
+use strict;
+
+use Bio::Index::Abstract;
+use Bio::Seq;
+
+@ISA = qw(Bio::Index::Abstract);
+
+#
+# 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 swisspfam 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.
+        $end,   # Offset from start of file of the end
+                # of the last found record.
+        $id,    # ID of last found record.
+	$acc,   # accession of last record. Also put into the index
+	$nid, $nacc, # new ids for the record just found
+        );
+
+    $begin = 0;
+    $end   = 0;
+
+    open SP, $file or $self->throw("Can't open file for read : $file");
+
+    # Main indexing loop
+    while (<SP>) {
+        if (/^>(\S+)\s+\|=*\|\s+(\S+)/) {
+	    $nid = $1;
+	    $nacc = $2;
+            my $new_begin = tell(SP) - length( $_ );
+            $end = $new_begin - 1;
+
+	    if( $id ) {
+		$self->add_record($id, $i, $begin, $end);
+		if( $acc ne $id ) {
+		    $self->add_record($acc, $i, $begin, $end);
+		}
+	    }
+            $begin = $new_begin;
+	    $id = $nid;
+	    $acc = $nacc;
+        }
+    }
+    # Don't forget to add the last record
+    $end = tell(SP);
+    $self->add_record($id, $i, $begin, $end) if $id;
+
+    close SP;
+    return 1;
+}
+
+
+=head2 fetch
+
+  Title   : fetch
+  Usage   : $index->fetch( $id )
+  Function: Returns a Bio::Seq object from the index
+  Example : $seq = $index->fetch( 'dJ67B12' )
+  Returns : Bio::Seq object
+  Args    : ID
+
+=cut
+
+sub fetch {
+    my( $self, $id ) = @_;
+    my $desc;
+    my $db = $self->db();
+    if (my $rec = $db->{ $id }) {
+        my( @record );
+        
+        my ($file, $begin, $end) = $self->unpack_record( $rec );
+        
+        # Get the (possibly cached) filehandle
+        my $fh = $self->_file_handle( $file );
+
+        # move to start
+        seek($fh, $begin, 0);
+
+        return $fh;
+    } else {
+	$self->throw("Unable to find a record for $id in SwissPfam flat file index");
+    }
+}
+
+1;