diff variant_effect_predictor/Bio/SeqIO/largefasta.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqIO/largefasta.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,170 @@
+# $Id: largefasta.pm,v 1.18 2002/12/27 19:42:32 birney Exp $
+# BioPerl module for Bio::SeqIO::largefasta
+#
+# Cared for by Jason Stajich
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+# _history
+# 
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::SeqIO::largefasta - method i/o on very large fasta sequence files
+
+=head1 SYNOPSIS
+
+Do not use this module directly.  Use it via the Bio::SeqIO class.
+
+=head1 DESCRIPTION
+
+This object can transform Bio::Seq objects to and from fasta flat
+file databases.
+
+This module handles very large sequence files by using the
+Bio::Seq::LargePrimarySeq module to store all the sequence data in
+a file.  This can be a problem if you have limited disk space on your
+computer because this will effectively cause 2 copies of the sequence
+file to reside on disk for the life of the
+Bio::Seq::LargePrimarySeq object.  The default location for this is
+specified by the L<File::Spec>-E<gt>tmpdir routine which is usually /tmp
+on UNIX.  If a sequence file is larger than the swap space (capacity
+of the /tmp dir) this could cause problems for the machine.  It is
+possible to set the directory where the temporary file is located by
+adding the following line to your code BEFORE calling next_seq. See
+L<Bio::Seq::LargePrimarySeq> for more information.
+
+    $Bio::Seq::LargePrimarySeq::DEFAULT_TEMP_DIR = 'newdir';
+
+=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 AUTHORS - Jason Stajich
+
+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 the code begin...
+
+package Bio::SeqIO::largefasta;
+use vars qw(@ISA $FASTALINELEN);
+use strict;
+# Object preamble - inherits from Bio::Root::Object
+
+use Bio::SeqIO;
+use Bio::Seq::SeqFactory;
+
+$FASTALINELEN = 60;
+@ISA = qw(Bio::SeqIO);
+
+sub _initialize {
+  my($self,@args) = @_;
+  $self->SUPER::_initialize(@args);    
+  if( ! defined $self->sequence_factory ) {
+      $self->sequence_factory(new Bio::Seq::SeqFactory
+			      (-verbose => $self->verbose(), 
+			       -type => 'Bio::Seq::LargePrimarySeq'));      
+  }
+}
+
+=head2 next_seq
+
+ Title   : next_seq
+ Usage   : $seq = $stream->next_seq()
+ Function: returns the next sequence in the stream
+ Returns : Bio::Seq object
+ Args    : NONE
+
+=cut
+
+sub next_seq {
+    my ($self) = @_;
+#  local $/ = "\n";
+    my $largeseq = $self->sequence_factory->create();
+    my ($id,$fulldesc,$entry);
+    my $count = 0;
+    my $seen = 0;
+    while( defined ($entry = $self->_readline) ) {
+	if( $seen == 1 && $entry =~ /^\s*>/ ) {
+	    $self->_pushback($entry);
+	    return $largeseq;
+	}
+#	if ( ($entry eq '>') || eof($self->_fh) ) { $seen = 1; next; }      
+	if ( ($entry eq '>')  ) { $seen = 1; next; }      
+	elsif( $entry =~ /\s*>(.+?)$/ ) {
+	    $seen = 1;
+	    ($id,$fulldesc) = ($1 =~ /^\s*(\S+)\s*(.*)$/)
+		or $self->warn("Can't parse fasta header");
+	    $largeseq->display_id($id);
+	    $largeseq->primary_id($id);	  
+	    $largeseq->desc($fulldesc);
+	} else {
+	    $entry =~ s/\s+//g;
+	    $largeseq->add_sequence_as_string($entry);
+	}
+	(++$count % 1000 == 0 && $self->verbose() > 0) && print "line $count\n";
+    }
+    if( ! $seen ) { return undef; } 
+    return $largeseq;
+}
+
+=head2 write_seq
+
+ Title   : write_seq
+ Usage   : $stream->write_seq(@seq)
+ Function: writes the $seq object into the stream
+ Returns : 1 for success and 0 for error
+ Args    : Bio::Seq object
+
+
+=cut
+
+sub write_seq {
+   my ($self,@seq) = @_;
+   foreach my $seq (@seq) {       
+     my $top = $seq->id();
+     if ($seq->can('desc') and my $desc = $seq->desc()) {
+	 $desc =~ s/\n//g;
+	 $top .= " $desc";
+     }
+     $self->_print (">",$top,"\n");
+     my $end = $seq->length();
+     my $start = 1;
+     while( $start < $end ) {
+	 my $stop = $start + $FASTALINELEN - 1;
+	 $stop = $end if( $stop > $end );
+	 $self->_print($seq->subseq($start,$stop), "\n");
+	 $start += $FASTALINELEN;
+     }
+   }
+
+   $self->flush if $self->_flush_on_write && defined $self->_fh;
+   return 1;
+}
+
+1;