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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqIO/raw.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,178 @@
+#-----------------------------------------------------------------------------
+# PACKAGE : Bio::SeqIO::raw
+# AUTHOR  : Ewan Birney <[e-mail]>
+# CREATED : Feb 16 1999
+# REVISION: $Id: raw.pm,v 1.15.2.1 2003/02/05 21:55:21 jason Exp $
+#            
+# Copyright (c) 1997-9 bioperl, Ewan Birney. All Rights Reserved.
+#           This module is free software; you can redistribute it and/or 
+#           modify it under the same terms as Perl itself.
+#
+# _History_
+#
+# Ewan Birney <[e-mail]> developed the SeqIO 
+# schema and the first prototype modules.
+#
+# This code is based on his Bio::SeqIO::Fasta module with
+# the necessary minor tweaks necessary to get it to read
+# and write raw formatted sequences made by
+# chris dagdigian <[e-mail]>
+#
+# October 18, 1999  Largely rewritten by Lincoln Stein
+#
+# Copyright Ewan Birney
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::SeqIO::raw - raw sequence file input/output stream
+
+=head1 SYNOPSIS
+
+Do not use this module directly.  Use it via the L<Bio::SeqIO> class.
+
+=head1 DESCRIPTION
+
+This object can transform Bio::Seq objects to and from raw flat
+file databases.
+
+
+=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://www.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
+
+  Ewan Birney   E<lt>[e-mail]<gt>
+  Lincoln Stein E<lt>[e-mail]<gt>
+
+=head1 CONTRIBUTORS
+
+  Jason Stajich 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::SeqIO::raw;
+use strict;
+use vars qw(@ISA);
+
+use Bio::SeqIO;
+use Bio::Seq::SeqFactory;
+
+@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'));      
+  }
+}
+
+=head2 next_seq
+
+ Title   : next_seq
+ Usage   : $seq = $stream->next_seq()
+ Function: returns the next sequence in the stream
+ Returns : Bio::Seq object
+ Args    :
+
+
+=cut
+
+sub next_seq{
+   my ($self,@args) = @_;
+   ## When its 1 sequence per line with no formatting at all,
+   ## grabbing it should be easy :)
+
+   my $nextline = $self->_readline();
+   if( !defined $nextline ){ return undef; }
+
+   my $sequence = uc($nextline);
+   $sequence =~ s/\W//g;
+
+   return  $self->sequence_factory->create(-seq => $sequence);
+}
+
+=head2 write_seq
+
+ Title   : write_seq
+ Usage   : $stream->write_seq($seq)
+ Function: writes the $seq object into the stream
+ Returns : 1 for success and 0 for error
+ Args    : Array of Bio::PrimarySeqI objects
+
+
+=cut
+
+sub write_seq {
+   my ($self,@seq) = @_;
+   foreach my $seq (@seq) {
+       $self->throw("Must provide a valid Bio::PrimarySeqI object") 
+	   unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
+     $self->_print($seq->seq, "\n") or return;
+   }
+   $self->flush if $self->_flush_on_write && defined $self->_fh;
+   return 1;
+}
+
+=head2 write_qual
+
+ Title   : write_qual
+ Usage   : $stream->write_qual($seq)
+ Function: writes the $seq object into the stream
+ Returns : 1 for success and 0 for error
+ Args    : Bio::Seq object
+
+
+=cut
+
+sub write_qual {
+   my ($self,@seq) = @_;
+   my @qual = ();
+   foreach (@seq) {
+     unless ($_->isa("Bio::Seq::SeqWithQuality")){
+        warn("You cannot write raw qualities without supplying a Bio::Seq::SeqWithQuality object! You passed a ", ref($_), "\n");
+        next;
+     } 
+     @qual = @{$_->qual};
+     if(scalar(@qual) == 0) {
+	    $qual[0] = "\n";
+     }
+     
+     $self->_print (join " ", @qual,"\n") or return;
+
+   }
+   return 1;
+}
+1;