[Bioperl-l] Remove gap only columns from alignment

Jason Stajich jason.stajich at duke.edu
Tue Feb 15 17:55:32 EST 2005

Passing in a second parameter, will only remove the all-gapped column
Like this:



  Title     : remove_gaps
  Usage     : $aln2 = $aln->remove_gaps('-'[,$all_gaps_columns])
  Function  : Creates an aligment with gaps removed
  Returns   : a Bio::SimpleAlign object
  Args      : a gap character(optional) if no specified,
                 taken from $self->gap_char,
                 optional $all_gaps_columns flag
                 indicates that only all-gaps columns should be deleted

Jason Stajich
jason.stajich at duke.edu

On Feb 16, 2005, at 3:21 AM, Goel, Manisha wrote:

> Hi All,
> I am currently using Bio::SimpleAlign to manipulate my alignments.
> I need to remove columns which are represented by gap characters in all
> seqs (similar to remove gap only columns in clustal), but the
> remove_gaps command seems to remove all columns even if a single
> sequence in the alignment has a gap at that position.
> Is there any other workaround to get this done ?
> Thanks,
> -Manisha
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
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