[Bioperl-l] remove gapped colums

[James Wasmuth]

 Hi Luisa,

try

$aln_nogaps = $aln->remove_columns(['gaps'])

-james


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Nematode Bioinformatics                  |
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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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 >