New software: gemucator Philip Fowler, 4th September 20184th September 2018 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 Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Related antimicrobial resistance computing tuberculosis
New preprint: automatically building a better bedaquiline catalogue 31st January 202531st January 2025 A catalogue recording whether individual mutations confer resistance or not to specified antibiotics is a… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
antimicrobial resistance New paper: Infection Inspection 10th September 202410th September 2024 This paper is the cumulation of a lot of hard work by an interdisciplinary team… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
antimicrobial resistance New software: pygsi 31st August 2018 Whenever a paper involving sequencing the genome of bacteria (or other species for that matter),… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More