Ambiguous bases about insilicoseq HOT 6 CLOSED

fixed in a6cf340

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caught another similar bug in the mut_sequence method. fixed in 8ecb2ab

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Hi,
Thanks for the great tool, really useful ! It looks like I stumbled across a variant of this bug, although the KeyError doesn't really make sense to me:
Traceback (most recent call last): File "/usr/local/lib/python3.6/site-packages/joblib/externals/loky/process_executor.py", line 418, in _process_worker r = call_item() File "/usr/local/lib/python3.6/site-packages/joblib/externals/loky/process_executor.py", line 272, in __call__ return self.fn(*self.args, **self.kwargs) File "/usr/local/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 567, in __call__ return self.func(*args, **kwargs) File "/usr/local/lib/python3.6/site-packages/joblib/parallel.py", line 225, in __call__ for func, args, kwargs in self.items] File "/usr/local/lib/python3.6/site-packages/joblib/parallel.py", line 225, in <listcomp> for func, args, kwargs in self.items] File "/usr/local/lib/python3.6/site-packages/iss/generator.py", line 59, in reads forward, reverse = simulate_read(record, ErrorModel, i) File "/usr/local/lib/python3.6/site-packages/iss/generator.py", line 134, in simulate_read forward.seq = ErrorModel.mut_sequence(forward, 'forward') File "/usr/local/lib/python3.6/site-packages/iss/error_models/__init__.py", line 100, in mut_sequence nucl_choices[position][nucl][0], KeyError: 'a'

I'm running 1.3.1 through Docker (docker:hadrieng/insilicoseq:1.3.1). This error disappear when I remove N's from my input genome, so I suspect it's something to do with how ambiguous base are handled ? (although I'm not sure what the error comes up as lower case a). Note that I got similar KeyError with 't", 'g', and 'c' (all lower case).

Thanks !

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Hi @simroux !

I think your error is more closely related to #73 , which I thought I fixed. I'll reopen the issue and let you know

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The genomes I am working with do have a small number of lower case nucleotides, so I may just have been lucky when the run succeeded after removing Ns :-)

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Should be fixed in 1.3.3

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