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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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Adding CGE-Predicted Phenotypes to staramr's Resfinder Output #167

Closed emarinier closed 1 year ago

emarinier commented 1 year ago

Adds CGE-predicted phenotypes to the output of staramr.

Example running with the README's tutorial data:

staramr search --pointfinder-organism salmonella -o out GCF_001478105.1.fasta

Example output:

Isolate ID  Gene    Predicted Phenotype CGE Predicted Phenotype %Identity   %Overlap    HSP Length/Total Length Contig  Start   End Accession   Sequence
GCF_001478105.1 blaCMY-2    ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone Amoxicillin,  Amoxicillin+Clavulanic acid,  Ampicillin,  Ampicillin+Clavulanic acid,  Cefotaxime,  Cefoxitin,  Ceftazidime,  Piperacillin,  Piperacillin+Tazobactam,  Ticarcillin,  Ticarcillin+Clavulanic acid 100.00  100.00  1146/1146   ref|NZ_JYVD01000056.1|  25020   26165   X91840  ATGATGAAAAAATCGTTA[...]
emarinier commented 1 year ago

What you have so far looks awesome. Great job getting this up and working so quickly 😄

The one comment I have so far is that you are storing a copy of the CGE gene drug table within the StarAMR data. Instead of doing this, I think it would be good to directly use the file installed as part of the ResFinder database (so that switching the ResFinder database used by StarAMR will also switch the gene-drug mapping to be consistent).

Awesome. Okay, I'll look into using the installed version of the database.