diff variant_effect_predictor/Bio/AlignIO/mase.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/AlignIO/mase.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,155 @@
+# $Id: mase.pm,v 1.9 2002/10/22 07:38:25 lapp Exp $
+#
+# BioPerl module for Bio::AlignIO::mase
+
+#	based on the Bio::SeqIO::mase module
+#       by Ewan Birney <[e-mail]>
+#       and Lincoln Stein  <[e-mail]>
+#
+#       and the SimpleAlign.pm module of Ewan Birney
+#
+# Copyright Peter Schattner
+#
+# You may distribute this module under the same terms as perl itself
+# _history
+# September 5, 2000
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::AlignIO::mase - mase sequence input/output stream
+
+=head1 SYNOPSIS
+
+Do not use this module directly.  Use it via the L<Bio::AlignIO> class.
+
+=head1 DESCRIPTION
+
+This object can transform L<Bio::Align::AlignI> objects to and from mase flat
+file databases.
+
+=head1 FEEDBACK
+
+=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 - Peter Schattner
+
+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::AlignIO::mase;
+use vars qw(@ISA);
+use strict;
+
+use Bio::AlignIO;
+
+@ISA = qw(Bio::AlignIO);
+
+
+=head2 next_aln
+
+ Title   : next_aln
+ Usage   : $aln = $stream->next_aln()
+ Function: returns the next alignment in the stream.
+ Returns : L<Bio::Align::AlignI> object
+ Args    : NONE
+
+=cut
+
+sub next_aln {
+    my $self = shift;
+    my $entry;
+    my $name;
+    my $start;
+    my $end;
+    my $seq;
+    my $add;
+    my $count = 0;
+    my $seq_residues;
+
+    my $aln =  Bio::SimpleAlign->new(-source => 'mase');
+
+
+    while( $entry = $self->_readline) {
+        $entry =~ /^;/ && next;
+	if(  $entry =~ /^(\S+)\/(\d+)-(\d+)/ ) {
+	    $name = $1;
+	    $start = $2;
+	    $end = $3;
+	} else {
+	    $entry =~ s/\s//g;
+	    $name = $entry;
+	    $end = -1;
+	}
+
+	$seq = "";
+
+	while( $entry = $self->_readline) {
+	    $entry =~ /^;/ && last;
+	    $entry =~ s/[^A-Za-z\.\-]//g;
+	    $seq .= $entry;
+	}
+	if( $end == -1) {
+	    $start = 1;
+
+	    $seq_residues = $seq;
+	    $seq_residues =~ s/\W//g;
+	    $end = length($seq_residues);
+	}
+
+	$add = new Bio::LocatableSeq('-seq'=>$seq,
+			    '-id'=>$name,
+			    '-start'=>$start,
+			    '-end'=>$end,
+			    );
+
+
+       $aln->add_seq($add);
+
+
+#  If $end <= 0, we have either reached the end of
+#  file in <> or we have encountered some other error
+#
+   if ($end <= 0) { undef $aln;}
+
+   }
+
+   return $aln;
+}
+
+
+
+=head2 write_aln
+
+ Title   : write_aln
+ Usage   : $stream->write_aln(@aln)
+ Function: writes the $aln object into the stream in mase format  ###Not yet implemented!###
+ Returns : 1 for success and 0 for error
+ Args    : L<Bio::Align::AlignI> object
+
+
+=cut
+
+sub write_aln {
+    my ($self,@aln) = @_;
+
+    $self->throw("Sorry: mase-format output, not yet implemented! /n");
+}
+
+1;