[Bioperl-l] Feature Request: add -alphabet to AlignIO arguments

Dexter Riley edbeaty at charter.net
Tue Aug 29 18:11:23 EDT 2006

Hello.  Currently, when you create a new Alignment using Bio::AlignIO->new(),
the method guesses the alphabet for each sequence using its base content. 
This means that sequences with a high percentage of degeneracies may be
misclassified as having a protein alphabet, resulting in an alignment object
with some 'dna' and some 'protein' sequences.  It is possible to manually
set the alphabet type on each sequence in the alignment, but it would be
simpler to add an -alphabet argument to the constructor, like so:
  my $in = Bio::AlignIO->new(
    -file => $filename, 
    -alphabet => 'dna',
    -format => 'clustalw');
If the -alphabet argument is not present, the constructor would guess the
alphabet type as before; if it is present, then that alphabet type would be
applied to each sequence in the alignment.
I'm not sure if this is the place for feature requests; if not, just let me
know and i'll post over there.  Also, I apologize if this got submitted
twice; I wasn't registered the first time.
Ed Beaty 

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