Closed cleme closed 11 years ago
We would need some additional information for this to be useful - can someone provide an example input that reproduces this issue (align_seqs.py
requires unaligned sequences, not an alignment).
Not really, I must have copied this from the trac site but I don't think I created the original bug report.
OK, in that case I'll close until we have an easy way to reproduce.
align_seqs.py gives an uninformative error message when it is passed as sequence collection instead of an alignment. The error message should be improved to assist users in debugging. The resulting error message is as follows:
Traceback (most recent call last): File "/home/caporaso/code/Qiime/scripts/align_seqs.py", line 171, in
main()
File "/home/caporaso/code/Qiime/scripts/align_seqs.py", line 157, in main
log_path=log_path,failure_path=failure_path)
File "/home/caporaso/code/Qiime/qiime/align_seqs.py", line 239, in call
aligned=DenseAlignment)
File "/home/caporaso/code/PyCogent/cogent/init.py", line 108, in LoadSeqs
label_to_name=label_to_name, *_constructor_kw)
File "/home/caporaso/code/PyCogent/cogent/core/alignment.py", line 1900, in init
super(DenseAlignment, self).init(_args, kwargs)
File "/home/caporaso/code/PyCogent/cogent/core/alignment.py", line 298, in init**
Alphabet=self.Alphabet)
File "/home/caporaso/code/PyCogent/cogent/core/alignment.py", line 419, in _names_seqs_order
seqs, names = conversion_f(data, Alphabet=Alphabet)
File "/home/caporaso/code/PyCogent/cogent/core/alignment.py", line 1801, in aln_from_kv_pairs
result = array(map(Alphabet.toIndices, seqs), array_type)