[Bioperl-l] AlignIO clustal

[Bernd Web]

Hi,

Using Bioperl 1.5.2 and AlignIO, I now run into an issue with a
clustalw alignment.
At the moment, I cannot update to a newer version, so am not sure this
problem still exists.

The problem is that the $aln object does not exists when the last
sequence in a block contains gaps only.
Anybody has seen this or knows a fix? Code and example input follows below.


Regards,
Bernd


use Bio::AlignIO;
my $in = Bio::AlignIO->new(-file => 'test.aln',
                           -format => 'clustalw');

my $out = Bio::AlignIO->new(-file => '>testerr.ALN',
                            -format => 'clustalw');
	
my $aln = $in->next_aln();
print $aln->length, "\n";

test.aln contains:

CLUSTAL W(1.81) multiple sequence alignment


QUERY/7-143            PETLE-ARINRATNPLNKEL--DWASI
7082547/1-128          ---------ERATNDMLIGP--DWAVN
1_3265048/1-0          ---------------------------
3265047/2-138          QTSLE-ALLLKATNSQNQNI--DTAAV
1_3265047/1-0          ---------------------------