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biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
GNU General Public License v2.0
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uninformative error message from align_seqs #248

Closed cleme closed 11 years ago

cleme commented 12 years ago

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)

gregcaporaso commented 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).

cleme commented 11 years ago

Not really, I must have copied this from the trac site but I don't think I created the original bug report.

gregcaporaso commented 11 years ago

OK, in that case I'll close until we have an easy way to reproduce.