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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqIO/ztr.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,173 @@
+# $Id: ztr.pm,v 1.8 2002/10/22 07:38:42 lapp Exp $
+# BioPerl module for Bio::SeqIO::ztr
+#
+# Cared for by Aaron Mackey <[e-mail]>
+#
+# Copyright Aaron Mackey
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::SeqIO::ztr - ztr trace sequence input/output stream
+
+=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 ztr trace
+files.
+
+=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 - Aaron Mackey
+
+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::ztr;
+use vars qw(@ISA $READ_AVAIL);
+use strict;
+# Object preamble - inherits from Bio::Root::Object
+
+use Bio::SeqIO;
+use Bio::Seq::SeqFactory;
+
+push @ISA, qw( Bio::SeqIO );
+
+sub BEGIN {
+    eval { require Bio::SeqIO::staden::read; };
+    if ($@) {
+	$READ_AVAIL = 0;
+    } else {
+	push @ISA, "Bio::SeqIO::staden::read";
+	$READ_AVAIL = 1;
+    }
+}
+
+sub _initialize {
+  my($self,@args) = @_;
+  $self->SUPER::_initialize(@args);  
+  if( ! defined $self->sequence_factory ) {
+      $self->sequence_factory(new Bio::Seq::SeqFactory(-verbose => $self->verbose(), -type => 'Bio::Seq::SeqWithQuality'));      
+  }
+
+  my ($compression) = $self->_rearrange([qw[COMPRESSION]], @args);
+  $compression = 2 unless defined $compression;
+  $self->compression($compression);
+
+  unless ($READ_AVAIL) {
+      Bio::Root::Root->throw( -class => 'Bio::Root::SystemException',
+			      -text  => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!"
+			    );
+  }
+}
+
+=head2 next_seq
+
+ Title   : next_seq
+ Usage   : $seq = $stream->next_seq()
+ Function: returns the next sequence in the stream
+ Returns : Bio::SeqWithQuality object
+ Args    : NONE
+
+=cut
+
+sub next_seq {
+
+    my ($self) = @_;
+
+    my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'ztr');
+
+    # create the seq object
+    $seq = $self->sequence_factory->create(-seq        => $seq,
+					   -id         => $id,
+					   -primary_id => $id,
+					   -desc       => $desc,
+					   -alphabet   => 'DNA',
+					   -qual       => $qual
+					   );
+    return $seq;
+}
+
+=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) = @_;
+
+    my $fh = $self->_fh;
+    foreach my $seq (@seq) {
+	$self->write_trace($fh, $seq, 'ztr' . $self->compression);
+    }
+
+    $self->flush if $self->_flush_on_write && defined $self->_fh;
+    return 1;
+}
+
+=head2 compression
+
+ Title   : compression
+ Usage   : $stream->compression(3);
+ Function: determines the level of ZTR compression
+ Returns : the current (or newly set) value.
+ Args    : 1, 2 or 3 - any other (defined) value will cause the compression
+           to be reset to the default of 2.
+
+
+=cut
+
+sub compression {
+
+    my ($self, $val) = @_;
+
+    if (defined $val) {
+	if ($val =~ m/^1|2|3$/o) {
+	    $self->{_compression} = $val;
+	} else {
+	    $self->{_compression} = 2;
+	}
+    }
+
+    return $self->{_compression};
+}
+
+1;