Adding CGE-Predicted Phenotypes to staramr's Resfinder Output

[emarinier]

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[...]

[apetkau]

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).

[emarinier]

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.

[apetkau]

This looks great. Thanks so much. Merging this in.