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iqbal-lab / Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop
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FP ERY on C00012757, don't think we should be calling this. #29

Closed Phelimb closed 9 years ago

Phelimb commented 9 years ago

{ "expected_depth": "88", "mean_read_length": "80", "species": { "S. aureus": "103" }, "susceptibility" :{ "Gentamicin": "S", "Penicillin": "R", "Methicillin": "S", "Trimethoprim": "S", "Erythromycin": "R", "FusidicAcid": "S", "Ciprofloxacin": "S", "Rifampicin": "S", "Tetracycline": "S", "Vancomycin": "S", "Mupirocin": "S", "Clindamycin": "R(inducible)" }, "called_variants" :{ }, "called_genes" :{ "blaZ" :{ "per_cov": "100", "median_cov": "204", "conf": "609", "induced_resistance": "Penicillin" }, "ermC" :{ "per_cov": "92", "median_cov": "1", "conf": "9", "induced_resistance": "Erythromycin" } }, "virulence_toxins" :{ "PVL": "negative" } }

iqbal-lab commented 9 years ago

Why not?

iqbal-lab commented 9 years ago

Is this a change or did we always make this call?

On 16 December 2014 at 18:19, Phelim Bradley notifications@github.com wrote:

{ "expected_depth": "88", "mean_read_length": "80", "species": { "S. aureus": "103" }, "susceptibility" :{ "Gentamicin": "S", "Penicillin": "R", "Methicillin": "S", "Trimethoprim": "S", "Erythromycin": "R", "FusidicAcid": "S", "Ciprofloxacin": "S", "Rifampicin": "S", "Tetracycline": "S", "Vancomycin": "S", "Mupirocin": "S", "Clindamycin": "R(inducible)" }, "called_variants" :{ }, "called_genes" :{ "blaZ" :{ "per_cov": "100", "median_cov": "204", "conf": "609", "induced_resistance": "Penicillin" }, "ermC" :{ "per_cov": "92", "median_cov": "1", "conf": "9", "induced_resistance": "Erythromycin" } }, "virulence_toxins" :{ "PVL": "negative" } }

— Reply to this email directly or view it on GitHub https://github.com/iqbal-lab/myKrobe-predictor/issues/29.

iqbal-lab commented 9 years ago

Hmm - we didn't make this call allegedly in commit 1f46ac5728f0a2a6888bcf379a84a9cdc472e772. See /Net/sequoia/data/zam_sequoia/staph_copy_from_banyan/validation_set/results_1f46ac5728f0a2a6888bcf379a84a9cdc472e772/FILE/_Net_sequoia_data_zam_sequoia_staph_copy_from_banyan_validation_set_filelists_C00012757.filelist/stdout

Except I can't find that commit anywhere!

iqbal-lab commented 9 years ago

Personally I'm not super worried about this call - we have 92% of the gene - that's cant be from sequencing errors

Phelimb commented 9 years ago

Yeah, I agree, I think I was just in variant mode when I submitted this so the 92% looked dodgy to me.