[Bioperl-l] Merging fragments in a simplealign

Chris Fields cjfields at illinois.edu
Fri Jan 22 08:40:57 EST 2010


May be something for the cook/scrapbook?

chris

On Jan 22, 2010, at 7:31 AM, Mark A. Jensen wrote:

> Here's one of my favorite tricks for this: XOR mask on gap symbol.
> MAJ
> 
> use Bio::SeqIO;
> use Bio::Seq;
> use strict; 
> my $seqio = Bio::SeqIO->new( -fh => \*DATA );
> 
> my $acc = $seqio->next_seq->seq ^ '-';
> while ($_ = $seqio->next_seq ) {
>   $acc ^= ($_->seq ^ '-');
> }
> my $mrg = Bio::Seq->new( -id => 'merged',
>   -seq => $acc ^ '-' );
> 1;
> 
> 
> __END__
>> seq2.234     
> QWERTYU-------------------
>> seq2.345     
> ----------ASDFGH----------
>> seq2.456     
> -------------------ZXCVBNM
> 
> ----- Original Message ----- From: "Albert Vilella" <avilella at gmail.com>
> To: <bioperl-l at lists.open-bio.org>
> Sent: Friday, January 22, 2010 8:07 AM
> Subject: [Bioperl-l] Merging fragments in a simplealign
> 
> 
>> Hi,
>> I would like to write a script that merges fragments in a Bio::SimpleAlign
>> object on the basis of
>> some $seq->display_name rule.
>> I basically want to start with something like this:
>> seq1.123     QWERTYUIOPASDFGHJKLZXCVBNM
>> seq2.234     QWERTYU-------------------
>> seq2.345     ----------ASDFGH----------
>> seq2.456     -------------------ZXCVBNM
>> And end with something like this:
>> seq1.123     QWERTYUIOPASDFGHJKLZXCVBNM
>> seq2.mrg     QWERTYU---ASDFGH---ZXCVBNM
>> Can people suggest any Bio::SimpleAlign methods that would help here?
>> Cheers,
>> Albert.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
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