Raw content of Bio::AlignIO::psi # $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 <jason@bioperl.org> # # 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. bioperl-l@bioperl.org - 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: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Jason Stajich Email jason@bioperl.org 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;