[Bioperl-l] Merging fragments in a simplealign
Chris Fields
cjfields at illinois.edu
Fri Jan 22 13:40:57 UTC 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
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
More information about the Bioperl-l
mailing list