search

ssi-dk / bifrost

MIT License
6 stars 6 forks source link

chewBBACA component for Bifrost #81

Closed finngl closed 1 year ago

finngl commented 2 years ago

We need a component that can run chewBBACA and write allele profiles to MongoDB.

finngl commented 2 years ago

There is some code in this repo that can JSONify the output from chewBBACA: https://gitlab.com/bfr_bioinformatics/chewieSnake/-/tree/jsonwriter Particularly scripts/json_writer.py

sofiehn commented 2 years ago

We'll need the following allele schemes

C. jejuni / C. coli cgMLST v1.0 https://pubmlst.org/bigsdb?db=pubmlst_campylobacter_seqdef&page=downloadAlleles&scheme_id=4&render=1

Escherichia/Shigella, cgMLST V1+HierCC V1 https://enterobase.warwick.ac.uk/species/ecoli/download_data

Salmonella, cgMLST V2+HierCC V1 https://enterobase.warwick.ac.uk/species/senterica/download_data

Yersinia, cgMLST V1+HierCC V1 https://enterobase.warwick.ac.uk/species/yersinia/download_data

Listeria, cgMLST1748 https://bigsdb.pasteur.fr/cgi-bin/bigsdb/bigsdb.pl?db=pubmlst_listeria_seqdef&page=downloadAlleles&scheme_id=3&render=1

The schemas needs to be run through chewBBACA.py PrepExternalSchema with the training file found under the chewBBACA installation fx /srv/data/tools/anaconda3/envs/shons/pkgs/chewbbaca-2.8.5-pyhdfd78af_0/site-packages/CHEWBBACA/prodigal_training_files to be updated

kriskiil commented 1 year ago

Blocked until we find a way to manage biodatabases. (SOFI#108)

finngl commented 1 year ago

Migrated to JIRA.