diff variant_effect_predictor/Bio/AlignIO/pfam.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/AlignIO/pfam.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,154 @@
+# $Id: pfam.pm,v 1.10 2002/10/22 07:38:26 lapp Exp $
+#
+# BioPerl module for Bio::AlignIO::pfam
+
+#	based on the Bio::SeqIO:: modules
+#       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::pfam - pfam 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 Bio::SimpleAlign objects to and from pfam 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::pfam;
+use vars qw(@ISA);
+use strict;
+
+use Bio::AlignIO;
+use Bio::SimpleAlign;
+@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 $acc;
+    my %names;
+
+    my $aln =  Bio::SimpleAlign->new(-source => 'pfam');
+
+    while( $entry = $self->_readline) {
+	chomp $entry;
+	$entry =~ /^\/\// && last;
+	if($entry !~ /^(\S+)\/(\d+)-(\d+)\s+(\S+)\s*/ ) {
+	    $self->throw("Found a bad line [$_] in the pfam format alignment");
+	    next;
+	}
+
+	$name = $1;
+	$start = $2;
+	$end = $3;
+	$seq = $4;
+
+
+	$add = new Bio::LocatableSeq('-seq'=>$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 $aln object into the stream
+ Returns : 1 for success and 0 for error
+ Args    : L<Bio::Align::AlignI> object
+
+
+=cut
+
+sub write_aln {
+   my ($self,@aln) = @_;
+   if( @aln > 1 ) { $self->warn("Only the 1st pfam alignment will be output since the format does not support multiple alignments in the same file"); }
+   my $aln = shift @aln;
+   if( ! $aln || ! $aln->isa('Bio::Align::AlignI')  ) { 
+       $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
+       next;
+   }
+   my ($namestr,$seq,$add);
+   my ($maxn);
+   $maxn = $aln->maxdisplayname_length();
+   
+   foreach $seq ( $aln->each_seq() ) {
+       $namestr = $aln->displayname($seq->get_nse());
+       $add = $maxn - length($namestr) + 2;
+       $namestr .= " " x $add;
+	  $self->_print (sprintf("%s  %s\n",$namestr,$seq->seq())) or return;
+   }
+   $self->flush() if $self->_flush_on_write && defined $self->_fh;
+   return 1;
+}
+
+1;