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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/AlignIO/prodom.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,137 @@
+# $Id: prodom.pm,v 1.8 2002/10/22 07:38:26 lapp Exp $
+#
+# BioPerl module for Bio::AlignIO::prodom
+
+#	based on the Bio::SeqIO::prodom 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::prodom - prodom 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 prodom 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::prodom;
+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 $entry;
+    my ($acc, $fake_id, $start, $end, $seq, $add, %names);
+
+    my $aln =  Bio::SimpleAlign->new(-source => 'prodom');
+
+    while( $entry = $self->_readline) {
+
+       if ($entry =~ /^AC\s+(\S+)\s*$/) {         #ps 9/12/00
+	   $aln->id( $1 );
+       }
+       elsif ($entry =~ /^AL\s+(\S+)\|(\S+)\s+(\d+)\s+(\d+)\s+\S+\s+(\S+)\s*$/){    #ps 9/12/00
+	   $acc=$1;
+	   $fake_id=$2;  # Accessions have _species appended
+	   $start=$3;
+	   $end=$4;
+	   $seq=$5;
+	
+	   $names{'fake_id'} = $fake_id;
+
+	   $add = new Bio::LocatableSeq('-seq'=>$seq,
+			       '-id'=>$acc,
+			       '-start'=>$start,
+			       '-end'=>$end,
+			       );
+	
+	   $aln->add_seq($add);
+       }
+       elsif ($entry =~ /^CO/) {
+	   # the consensus line marks the end of the alignment part of the entry
+	   last;
+       }
+   }
+
+#  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 $aln object into the stream in prodom format  ###Not yet implemented!###
+ Returns : 1 for success and 0 for error
+ Args    : L<Bio::Align::AlignI> object
+
+
+=cut
+
+sub write_aln {
+    my ($self,@aln) = @_;
+
+    $self->throw("Sorry: prodom-format output, not yet implemented! /n");
+}
+
+1;