[Bioperl-l] Merging fragments in a simplealign

Albert Vilella avilella at gmail.com
Fri Jan 22 08:07:26 EST 2010


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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