[Bioperl-l] remove gapped colums

[Shawn Hoon]

Sorry after re-reading my last mail it didn't seem very clear.
You can do this:

use Bio::AlignIO;
my $aio = Bio::AlignIO->new(-file=>"myalign.txt",-format=>'clustalw');
my $aln = $aio->next_aln;

my $new_aln = $aln->remove_gaps;

my $aout = Bio::AlignIO->new(-fh=>\*STDOUT,-format=>'clustalw');
$aout->write_aln($new_aln);



On May 11, 2004, at 8:04 AM, luisa pugliese wrote:

> Hi,
>    I am new at bioperl and I am working on alignments. I am splitting 
> a multiple alignment into several pairwise alignments and I would like 
> to remove the columns in which there are gaps in all the sequences. 
> Does anybody knows if a method exists doing this or a method finding 
> the columns in which there are gaps in all the sequences similar 
> gap_line that find the gaps present in any columns?
> Thank you
> Luisa Pugliese
> =============================
> Luisa Pugliese, Ph.D.
> luisa.pugliese at safan-bioinformatics.it
> S.A.F.AN. BIOINFORMATICS
> Corso Tazzoli 215/13 -10137 Torino
> tel +39 011 3026230
> cell. +39 333 6130644
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