Stopiteration
Closed this issue · 3 comments
Hi,
I am running straingr Prepare a concatenated reference
##############################################################
(straingr prepare-ref -s path/to/straingst/*.tsv
-p "path/to/refdir/{ref}.fa.gz"
-S path/to/straingst_db/similarities.tsv
-o refs_concat.fasta)
##############################################################
I got this error message
####################################################################################################
File "/cluster/home/ahmedbar/.conda/envs/strainge/lib/python3.7/site-packages/strainge/io/utils.py", line 109, in parse_straingst
next(result_file)
StopIteration
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/cluster/home/ahmedbar/.conda/envs/strainge/bin/straingr", line 11, in
sys.exit(straingr_cli())
File "/cluster/home/ahmedbar/.conda/envs/strainge/lib/python3.7/site-packages/strainge/cli/main.py", line 110, in call
self.run(args)
File "/cluster/home/ahmedbar/.conda/envs/strainge/lib/python3.7/site-packages/strainge/cli/registry.py", line 83, in run
rc = subcommand_func(**args_dict)
File "/cluster/home/ahmedbar/.conda/envs/strainge/lib/python3.7/site-packages/strainge/cli/straingr.py", line 154, in call
parse_straingst(f))
File "/cluster/home/ahmedbar/.conda/envs/strainge/lib/python3.7/collections/init.py", line 655, in update
_count_elements(self, iterable)
File "/cluster/home/ahmedbar/.conda/envs/strainge/lib/python3.7/site-packages/strainge/cli/straingr.py", line 153, in
straingst_counter.update(strain['strain'] for strain in
RuntimeError: generator raised StopIteration
####################################################################################################
Could you please help with that?
Oh I think I haven't updated prepare-ref yet to support the new StrainGST output format, I'll fix this soon!
Thanks.
Could you please inform me as soon as you fix it?
I will be waiting for you.
Please fix it ASAP I need it urgently!
A new version is available on PyPI, bioconda will be updated soon. Please list only the *.strains.tsv files now when running prepare-ref.