Bio::AlignIO
psi
Summary
Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
This module will parse PSI-BLAST output of the format seqid XXXX
Description
This is a parser for psi-blast blocks.
Methods
Methods description
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 |
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the NCBI psi-format object (.aln) into the stream
Returns : 1 for success and 0 for error
Args : Bio::Align::AlignI object
Bio::Align::AlignI |
Methods code
sub next_aln
{ my ($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 $aln;} | sub write_aln
{ my ($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;} | General documentation
User feedback is an integral part of the evolution of this and other
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the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
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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:
http://bugzilla.open-bio.org/
| AUTHOR - Jason Stajich | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : new
Usage : my $obj = new Bio::AlignIO::psi();
Function: Builds a new Bio::AlignIO::psi object
Returns : Bio::AlignIO::psi
Args :