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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/AlignIO/stockholm.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $Id: stockholm.pm,v 1.10.2.1 2003/03/14 09:14:59 heikki Exp $
+#
+# BioPerl module for Bio::AlignIO::stockholm
+
+#	based on the Bio::SeqIO::stockholm 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::stockholm - stockholm 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
+stockholm 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 CONTRIBUTORS
+
+Andreas Kahari, [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::stockholm;
+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 $entry;
+
+    my ($start,$end,%align,$name,$seqname,$seq,$count,
+	%hash,%c2name, %accession, $no);
+
+    # in stockholm format, every non-blank line that does not start
+    # with '#=' is an alignment segment; the '#=' lines are mark up lines.
+    # Of particular interest are the '#=GF <name/st-ed> AC <accession>'
+    # lines, which give accession numbers for each segment
+
+    my $aln =  Bio::SimpleAlign->new(-source => 'stockholm');
+
+    while( defined($entry = $self->_readline) ) {
+        $entry !~ /\w+/ && next;
+
+	if ($entry =~ /^#\s*STOCKHOLM\s+/) {
+	    last;
+	}
+	else {
+	    $self->throw("Not Stockholm format: Expecting \"# STOCKHOLM 1.0\"; Found \"$_\"");
+	}
+    }
+#
+#    Next section is same as for selex format
+#
+    while( defined($entry = $self->_readline) ) {
+	# Double slash (//) signals end of file.  The flat Pfam-A data from
+	# ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Pfam-A.full.gz consists
+	# of several concatenated Stockholm-formatted files.  The following
+	# line makes it possible to parse it without this module trying to
+	# read the whole file into memory.  Andreas Kähäri 10/3/2003.
+	last if $entry =~ /^\/\//;
+
+	# Extra bonus:  Get the name of the alignment.
+	# Andreas Kähäri 10/3/2003.
+	if ($entry =~ /^#=GF\s+AC\s+(\S+)/) {
+	    $aln->id($1);
+	    next;
+	}
+
+	$entry =~ /^#=GS\s+(\S+)\s+AC\s+(\S+)/ && do {
+	    $accession{ $1 } = $2;
+	    next;
+	};
+	$entry =~ /^([A-Za-z.-]+)$/ && ( $align{$name} .= $1 ) && next; 
+	$entry !~ /^([^#]\S+)\s+([A-Za-z.-]+)\s*/ && next;
+
+	
+	$name = $1;
+	$seq = $2;
+
+	if( ! defined $align{$name}  ) {
+	    $count++;
+	    $c2name{$count} = $name;
+	}
+	$align{$name} .= $seq;
+    }
+
+    # ok... now we can make the sequences
+
+     foreach $no ( sort { $a <=> $b } keys %c2name ) {
+	$name = $c2name{$no};
+
+	if( $name =~ /(\S+)\/(\d+)-(\d+)/ ) {
+	    $seqname = $1;
+	    $start = $2;
+	    $end = $3;
+	} else {
+	    $seqname=$name;
+	    $start = 1;
+	    $end = length($align{$name});
+	}
+	$seq = new Bio::LocatableSeq('-seq'=>$align{$name},
+			    '-id'=>$seqname,
+			    '-start'=>$start,
+			    '-end'=>$end,
+			    '-type'=>'aligned',
+				     '-accession_number' => $accession{$name},
+
+			    );
+
+       $aln->add_seq($seq);
+
+   }
+
+#  If $end <= 0, we have either reached the end of
+#  file in <fh> or we have encountered some other error
+#
+   if ($end <= 0) { undef $aln;}
+
+   return $aln;
+}
+
+
+=head2 write_aln
+
+ Title   : write_aln
+ Usage   : $stream->write_aln(@aln)
+ Function: writes the $aln object into the stream in stockholm format  ###Not yet implemented!###
+ Returns : 1 for success and 0 for error
+ Args    : L<Bio::Align::AlignI> object
+
+
+=cut
+
+sub write_aln {
+    my ($self,@aln) = @_;
+
+    $self->throw("Sorry: stockholm-format output, not yet implemented! /n");
+}
+
+1;