[Bioperl-l] gap characters in SimpleAlign objects

[Ewan Birney]

On Wed, 18 Feb 2004, Nathan Haigh wrote:

> I've been using the clustalw module for creating alignment, and I've just
> realised that when you output the alignment the gap character is a "." not a
> "-".
> This is most annoying because I am adding support to this module for
> generating trees via clustalw, and clustalw removes these "." characters. Is
> there a method for changing these gap characters to "-". I have seen the
> gap_char method in the SimpleAlign module, but this seems only to designate
> a particular character as a gap character, and does not actually change the
> character.
> 
> Any ideas on how to do this substitution, and where in BioPerl does this
> assignment get made in the first place, since the default gap char for
> clustalw output is "-" not "."

To fix (short term): Loop over the sequences making a new SimpleAlign
object with LocatableSeqs and s/\./-/ on the seq strings



How are you reading in Clustalw alignments? The Bio::AlignIO::clustalw 
doesn't touch the gap characters:


    foreach my $name ( sort { $order{$a} <=> $order{$b} } keys %alignments 
) {
        if( $name =~ /(\S+):(\d+)-(\d+)/ ) {
            ($sname,$start,$end) = ($1,$2,$3);      
        } else {
            ($sname, $start) = ($name,1);
            my $str  = $alignments{$name};
            $str =~ s/[^A-Za-z]//g;
            $end = length($str);
        }
        my $seq = new Bio::LocatableSeq('-seq'   => $alignments{$name},
                                         '-id'    => $sname,
                                         '-start' => $start,
                                         '-end'   => $end);
 


($alignments{$name} has no regex put on it earlier either)



> 
> Thanks
> Nathan
> 
> 
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> 

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