[Bioperl-l] SimpleAlign/AlignIO

Bernd Web bernd.web at gmail.com
Thu Sep 18 13:34:49 EDT 2008


Possibly I overlooked this, but is it not possible to supply an
alphabet to SimpleAlign?
When SimpleAlign starts making sequence objects _guess_alphabet is
executed and in case the sequence (slice) only contains gaps a warning
is raised as the alphabet cannot be guessed.
As all sequences in the alignment (generally) would be of the same
type, it could be good to set the alpabet for the alignment; this also
would prevent the executing of _guess_alphabet for all sequences. Is
this possible?


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