antimicrobial resistance computing tuberculosis

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.

> --mutation rpoB_S450L
761153 t
761154 c
761155 g

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

> --location 761153

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.

> --mutation rpoB_K450L
Traceback (most recent call last):
File "/Users/fowler/Library/Python/3.5/bin/", line 6, in <module>
exec(compile(open(__file__).read(), __file__, 'exec'))
File "/Users/fowler/packages/gemucator/bin/", line 14, in <module>
File "/Users/fowler/packages/gemucator/gemucator/", 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


By Philip Fowler

Philip W Fowler is a computational biophysicist studying antimicrobial resistance working at the John Radcliffe Hospital in Oxford.

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