[Bioperl-l] Finding the Sequence List in an Alignment

Jason Stajich jason at bioperl.org
Fri Jul 27 00:28:36 EDT 2007


Have you tried reading the documentation for the Bio::SimpleAlign object?

for my $seq ( $aln->each_seq ) {
 print $seq->display_id, "\n";
}

I'd appreciate if you added some of your questions with the answers to the
FAQ or to other places on the wiki so that other people can benefit from
your learning here.


On 7/26/07, Munirul Islam <ba6450 at wayne.edu> wrote:
>
> Thanks.  The error is removed now.
>
> I have a question.  Is there any function that I can use to get the
> sequence list (human, chimp, etc.) after loading an alignment from file?
>
> Munir
>
> ---- Original message ----
> >Date: Thu, 26 Jul 2007 17:12:03 -0700
> >From: "Jason Stajich" <jason at bioperl.org>
> >Subject: Re: [Bioperl-l] Alignment works with codeml (not loading in
> bioperl)
> >To: "Munirul Islam" <ba6450 at wayne.edu>
> >Cc: bioperl-l at lists.open-bio.org
> >
> >You can try and pass in -interleaved => 0 as another option when you
> >init your AlignIO object.
> >
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>



-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki/User:Jason


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