[Bioperl-l] small change to Bio::Align::Utilities
skirov at utk.edu
Mon Apr 19 10:40:28 EDT 2004
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.
>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",
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