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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/AlignIO/psi.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,166 @@
+# $Id: psi.pm,v 1.6 2002/12/23 19:36:39 jason Exp $
+#
+# BioPerl module for Bio::AlignIO::psi
+#
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files
+
+=head1 SYNOPSIS
+
+This module will parse PSI-BLAST output of the format seqid XXXX  
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=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
+the Bioperl mailing list.  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
+of the bugs and their resolution. Bug reports can be submitted via
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Jason Stajich
+
+Email [e-mail]
+
+Describe contact details here
+
+=head1 CONTRIBUTORS
+
+Additional contributors names and emails here
+
+=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::psi;
+use vars qw(@ISA $BlockLen $IdLength);
+use strict;
+
+$BlockLen = 100; 
+$IdLength = 13;
+
+# Object preamble - inherits from Bio::Root::Root
+
+use Bio::SimpleAlign;
+use Bio::AlignIO;
+use Bio::LocatableSeq;
+
+@ISA = qw(Bio::AlignIO);
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::AlignIO::psi();
+ Function: Builds a new Bio::AlignIO::psi object 
+ Returns : Bio::AlignIO::psi
+ Args    :
+
+=cut
+
+=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) = @_;
+    my $aln;
+    my %seqs;
+    my @order;
+    while( defined ($_ = $self->_readline ) ) {
+	next if( /^\s+$/);
+	if( !defined $aln ) {
+	    $aln = new Bio::SimpleAlign;
+	}
+	my ($id,$s) = split;
+	push @order, $id if( ! defined $seqs{$id});
+	$seqs{$id} .= $s;
+    }
+    foreach my $id ( @order) {
+	my $seq = new Bio::LocatableSeq(-seq => $seqs{$id},
+					-id  => $id,
+					-start => 1,
+					-end   => length($seqs{$id}));
+	$aln->add_seq($seq);
+    }
+    return $aln;
+}
+
+=head2 write_aln
+
+ Title   : write_aln
+ Usage   : $stream->write_aln(@aln)
+ Function: writes the NCBI psi-format object (.aln) into the stream
+ Returns : 1 for success and 0 for error
+ Args    : L<Bio::Align::AlignI> object
+
+
+=cut
+
+sub write_aln {
+    my ($self,$aln) = @_;
+    unless( defined $aln && ref($aln) && 
+	    $aln->isa('Bio::Align::AlignI') ) {
+	$self->warn("Must provide a valid Bio::Align::AlignI to write_aln");
+	return 0;
+    }
+    my $ct = 0;
+    my @seqs = $aln->each_seq;
+    my $len = 1;
+    my $alnlen = $aln->length;
+    my $idlen = $IdLength;
+    my @ids = map { substr($_->display_id,0,$idlen) } @seqs;
+    while( $len < $alnlen ) {
+	my $start = $len;
+	my $end   = $len + $BlockLen;
+	if( $end > $alnlen ) { $end = $alnlen; }
+	my $c = 0;
+	foreach my $seq ( @seqs ) {
+	    $self->_print(sprintf("%-".$idlen."s %s\n",
+				  $ids[$c++],
+				  $seq->subseq($start,$end)));
+	}
+	$self->_print("\n");
+	$len += $BlockLen+1;
+    }
+    $self->flush if $self->_flush_on_write && defined $self->_fh;
+    return 1;
+}
+
+1;