New software: gemucator

Short for “Genbank Mutation Locator”. A simple Python3 package that if you pass it a mutation it will give you the location in the specified genbank file.

> gemucator-run.py --mutation rpoB_S450L
rpoB_S450L:
761153 t
761154 c
761155 g

(H37rV.gbk for M. tuberculosis is loaded by default). Or you can go the other way

> gemucator-run.py --location 761153
rpoB_S450

It has no unit testing, but checks that the mutation is consistent with the genbank file which means you can check if your genetic catalogue is correct.

> gemucator-run.py --mutation rpoB_K450L
Traceback (most recent call last):
File "/Users/fowler/Library/Python/3.5/bin/gemucator-run.py", line 6, in <module>
exec(compile(open(__file__).read(), __file__, 'exec'))
File "/Users/fowler/packages/gemucator/bin/gemucator-run.py", line 14, in <module>
(locations,bases)=tb_reference_genome.locate_mutation(options.mutation)
File "/Users/fowler/packages/gemucator/gemucator/core.py", line 127, in locate_mutation
assert before==bases.translate(), "wildtype amino acid specified in mutation does not match the "+self.genbank_file+" genbank file"
AssertionError: wildtype amino acid specified in mutation does not match the config/H37rV.gbk genbank file

 

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