Bio::AlignIO psi
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Summary
Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files
Package variables
No package variables defined.
Included modules
Bio::LocatableSeq
Bio::SimpleAlign
Inherit
Bio::AlignIO
Synopsis
This module will parse PSI-BLAST output of the format seqid XXXX
Description
This is a parser for psi-blast blocks.
Methods
next_alnDescriptionCode
write_alnDescriptionCode
Methods description
next_alncode    nextTop
 Title   : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream
Returns : Bio::Align::AlignI object
Args : NONE
See Bio::Align::AlignI
write_alncodeprevnextTop
 Title   : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the NCBI psi-format object (.aln) into the stream
Returns : 1 for success and 0 for error
Args : Bio::Align::AlignI object
Bio::Align::AlignI
Methods code
next_alndescriptionprevnextTop
sub next_aln {
    my ($self) = @_;
    my $aln;
    my %seqs;
    my @order;
    while( defined ($_ = $self->_readline ) ) {
	next if( /^\s+$/);
	if( !defined $aln ) {
	    $aln = Bio::SimpleAlign->new();
	}
	my ($id,$s) = split;
	push @order, $id if( ! defined $seqs{$id});
	$seqs{$id} .= $s;
    }
    foreach my $id ( @order) {
    my $gaps = $seqs{$id} =~ tr/-/-/;
	my $seq = Bio::LocatableSeq->new(-seq => $seqs{$id},
					-id  => $id,
					-start => 1,
					-end   => length($seqs{$id}) - $gaps,
					 -alphabet => $self->alphabet,
                    );
	$aln->add_seq($seq);
    }
    return $aln if defined $aln && $aln->num_sequences;
	return $aln;
}
write_alndescriptionprevnextTop
sub write_aln {
	my ($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 + 1) ) {
		my $start = $len;
		my $end   = $len + $BlockLen;
		$end = $alnlen if ( $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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
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
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 Title   : new
Usage : my $obj = Bio::AlignIO::psi->new();
Function: Builds a new Bio::AlignIO::psi object
Returns : Bio::AlignIO::psi
Args :