[BioPython] Alphabet Checking
Renato Alves
rjalves at igc.gulbenkian.pt
Mon Jan 28 17:42:05 UTC 2008
/var/lib/python-support/python2.4/Bio/Translate.py in
translate_to_stop(self, seq)
34 def translate_to_stop(self, seq):
35 # This doesn't have a stop encoding
---> 36 assert seq.alphabet == self.table.nucleotide_alphabet, \
37 "cannot translate from given alphabet (have %s,
need %s)" %\
38 (seq.alphabet, self.table.nucleotide_alphabet)
AssertionError: cannot translate from given alphabet (have
IUPACAmbiguousDNA(), need IUPACAmbiguousDNA())
Aren't those two exactly equal?
Matching references doesn't seem to work as expected :(
What I did:
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from Bio import Translate
from Bio import Seq
a=Seq.Seq("ATCGGATGA...ATGCAGT",alphabet=IUPACAmbiguousDNA())
b=Translate.ambiguous_dna_by_id[11]
b.translate_to_stop(a) ... error pops out
The only way around I was able to find is:
b.table.nucleotide_alphabet=a.alphabet
I guess this is a bad day :( it's the second clash with the Translate
module in the same day :|
Should I report this as bug?
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