[Bioperl-l] small change to Bio::Align::Utilities

Stefan Kirov skirov at utk.edu
Mon Apr 19 10:40:28 EDT 2004

Hi Albert,
This certainly can be a problem. Actually I believe this problem should 
be handled by Bio::AlignIO, where each format specific parser will 
convert the gap character to a standard, "-" for example in the 
resulting Bio::Align::AliignI object.. And also account for cases like 
the one you mentioned. Then we can take my correction out.
In any case aa_to_dna_aln did not care about . so you would end up with 
a shortened sequence.

avilella wrote:

>On Fri, 2004-04-16 at 18:00, Stefan Kirov wrote:
>>Hope this does not break anything else... Just introduced "." as a 
>>possible gap character to be expected along with "-" in aa_to_dna_aln.
>Just to mention that, in some file formats, "." means "the same
>character as the first sequence",
>    Albert.

More information about the Bioperl-l mailing list