[Bioperl-l] SimpleAlign

Bernd Web bernd.web at gmail.com
Fri Jun 9 09:23:21 EDT 2006


Hi,

Two queries with respect to SimpleAlign. I am using the following code
based on the POD.

my $in  = Bio::AlignIO->newFh(-file => $file, -format => 'fasta');
my $out = Bio::AlignIO->newFh('-format' => 'clustalw');
print $out $_ while <$in>;

1) is it possible to set set_displayname_flat() globally without doing
$_->set_displayname_flat() per alignment.

2) My input files have an ID and description line for each seq in the
alignment. When the file is converted I loose the description line. I
know I can get the description of the sequences (e.g.
$aln->get_seq_by_pos(2)->description()).
How could I export the complete fasta defline including the
description (I realize that general clustal format has a limit on the
number of characters, but still).

Regards,
Bernd


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