[Bioperl-l] AlignIO clustal

Bernd Web bernd.web at gmail.com
Fri Apr 3 09:47:23 EDT 2009


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.


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

7082547/1-128          ---------ERATNDMLIGP--DWAVN
1_3265048/1-0          ---------------------------
3265047/2-138          QTSLE-ALLLKATNSQNQNI--DTAAV
1_3265047/1-0          ---------------------------

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