[Bioperl-l] Merging fragments in a simplealign

Albert Vilella avilella at gmail.com
Fri Jan 22 12:50:57 EST 2010


Or to rephrase my answer, what is the closest way for the code below that
already exists?

On Fri, Jan 22, 2010 at 4:04 PM, Albert Vilella <avilella at gmail.com> wrote:

> Is there/should be a 'have_pairwise_overlap' method similar to this?
>
> # $seq1 and $seq3 have matching ids
> my $seq1 = $aln->each_seq_by_id($seq1->display_id);
> my $seq3 = $aln->each_seq_by_id($seq3->display_id);
>
> my $ret = $aln->have_pairwise_overlap($seq1,$seq3);
>
>
> On Fri, Jan 22, 2010 at 1:40 PM, Chris Fields <cjfields at illinois.edu>wrote:
>
>> 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.
>> >> _______________________________________________
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>> >> Bioperl-l at lists.open-bio.org
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>> >>
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>>
>>
>


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