[Bioperl-l] Parsing needle/water output

[Mahmut Uludag]

> > > yes, i tried to read the documentation about
> > > Bio::AlignIO::emboss, but there
> > > is not much in it.So is like i can call the same functions
> > > which are used in
> > > searchIO. I need start and end position of the pairwise alignment.

Hi Shalabh,

I copied below an example script that prints start and end position of
sequences used for constructing pairwise alignment by EMBOSS 'water'
program. After your last email this became an unnecessary example but i
thought it would be useful for people with similar questions in the
future.

Regards,
Mahmut


use Bio::Factory::EMBOSS;
use Bio::Seq;
use Bio::AlignIO;

my $aseq = Bio::Seq->new( -id => 'seq1', -seq => 'AACATGTAGGGATAG' );
my $bseq = Bio::Seq->new( -id => 'seq2', -seq => 'GCATGTTTAGATAG' );
my $factory      = new Bio::Factory::EMBOSS;
my $water        = $factory->program("water");
my $wateroutfile = 'out.water';

$water->run(
	{
		-asequence => $aseq,
		-bsequence => $bseq,
		-gapopen   => '10.0',
		-gapextend => '0.5',
		-outfile   => $wateroutfile
	}
);

my $alnin = new Bio::AlignIO(
	-format => 'emboss',
	-file   => $wateroutfile
);

while ( my $aln = $alnin->next_aln ) {
	# process the alignment -- Bio::SimpleAlign objects
	foreach $seq ( $aln->each_seq() ) {
		print "\n" . $seq->display_id;
		print " " . $seq->start . " " . $seq->end;
	}
	print "\n" . $aln->percentage_identity;
	print "\n" . $aln->consensus_string(50) . "\n";
}