[Bioperl-l] Res: extract overhangs from Clustalw

[Roy Chaudhuri]

Hi Rondon,

Please remember to cc the mailing list when you reply, that way others 
can chip in with an answer.

The $endgapfree variable contains a Bio::SimpleAlign object, not a 
Bio::AlignIO. So you can get rid of the while loop and just say:

$out->write_aln($endgapfree);

Cheers,
Roy.

On 15/02/2011 18:05, Rondon Neto wrote:
> Thank you! Sorry my poor question.
>
> I have gaps in the central region and want to keep them. I use your
> suggestion and that works. I tried to print the alignment without
> success, so I'm thinking to save it in a new file, like we do in SeqIO,
> but its not working. Is that the way? see my code:
>
> -----------------------------------------------
> #/usr/bin/perl
> use warnings;
> use strict;
> use Bio::AlignIO;
>
> my $str = Bio::AlignIO->new('-file' => $ARGV[0]);
> my $aln = $str->next_aln();
> $aln->gap_line=~/^(-*).*[^-](-*)$/;
> my $endgapfree=$aln->remove_columns([0,length($1)-1],
> [$aln->length-length($2), $aln->length-1]);
>
> my $out = Bio::AlignIO->new(-file => ">test.out",
> -format => 'clustalw');
>
> while ( my $aln = $endgapfree->next_aln() ) {
> $out->write_aln($aln);
> }
>
> exit;
> ------------------------------------------------
>
> Thank you again,
>
> Rondon Neto
>
>
>
> ------------------------------------------------------------------------
> *De:* Roy Chaudhuri <roy.chaudhuri at gmail.com>
> *Para:* Rondon Neto <rondonbio at yahoo.com.br>
> *Cc:* Jordi Durban <jordi.durban at gmail.com>; bioperl-l at lists.open-bio.org
> *Enviadas:* Terça-feira, 15 de Fevereiro de 2011 10:19:00
> *Assunto:* Re: [Bioperl-l] extract overhangs from Clustalw
>
> Hi Rondon,
>
> I'm assuming you mean "how do I remove columns with gaps at either end
> of the alignment?" (since your alignment should be flush if it has come
> from ClustalW). In future, when you ask questions on the list please try
> and give as much information as possible, that way we do not have to
> guess at what you mean.
>
> If those are the only gaps in the alignment, then this will work:
>
> my $gapfree=$aln->remove_gaps;
>
> However, if there are gaps in the central region that you want to keep,
> then try something like this:
>
> $aln->gap_line=~/^(-*).*[^-](-*)$/;
> my $endgapfree=$aln->remove_columns([0,length($1)-1],
> [$aln->length-length($2), $aln->length-1]);
>
> This will not work correctly if there aren't gaps at both ends of the
> alignment, so you may have to add in a few checks if you can't make that
> assumption.
>
> Cheers,
> Roy.
>
> On 14/02/2011 20:52, Jordi Durban wrote:
>  > What do you mean by "overhangs"?
>  > Have ypu heard about Extending Bio::Tools::Run::Clustalw?
>  > hope this helps.
>  > 2011/2/14 Rondon Neto<rondonbio at yahoo.com.br
> <mailto:rondonbio at yahoo.com.br>>
>  >
>  >> How to extract overhangs from Clustalw alignments and return the aln
> file
>  >> without the overhangs? I'm trying to use Bio::AlignIO, but Im confused.
>  >> Thank you very much.
>  >>
>  >> Rondon
>  >>
>  >>
>  >>
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