[Bioperl-l] remove gapped colums

[Shawn Hoon]

There are 2 methods that returns alignments with gaps or alignments 
removed. Try it and see this works for you.

        remove_columns

         Title     : remove_column
         Usage     : $aln2 = $aln->remove_columns(['mismatch','weak'])
         Function  :
                     Creates an aligment with columns removed 
corresponding to
                     the specified criteria.
         Returns   : a L<Bio::SimpleAlign> object
         Args      : array ref of types, 
'match'|'weak'|'strong'|'mismatch'|'gaps'

        remove_gaps

         Title     : remove_gaps
         Usage     : $aln2 = $aln->remove_gaps('-')
         Function  :
                     Creates an aligment with gaps removed
         Returns   : a L<Bio::SimpleAlign> object
         Args      : a gap character(optional) if no specified,
                     taken from $self->gap_char

cheers,
shawn


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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