Mercurial > repos > nml > mykrobe_parser

view test-data/prediction_2019/output-report.csv @ 6:8e7e5a660942 draft

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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
author nml
date Fri, 22 Sep 2023 17:24:02 +0000
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"file","Mykrobe_fabG1","Mykrobe_katG","Mykrobe_ahpC","Mykrobe_inhA","Mykrobe_ndh","Isoniazid_R_mutations","Isoniazid_Prediction","Mykrobe_rpoB","Rifampicin_R_mutations","Rifampicin_Prediction","Mykrobe_embB","Mykrobe_embA","Ethambutol_R_mutations","Ethambutol_Prediction","Mykrobe_pncA","Mykrobe_rpsA","Pyrazinamide_R_mutations","Pyrazinamide_Prediction","Mykrobe_Ofloxacin_gyrA","Ofloxacin_R_mutations","Ofloxacin_Prediction","Mykrobe_Moxifloxacin_gyrA","Moxifloxacin_R_mutations","Moxifloxacin_Prediction","Mykrobe_Ciprofloxacin_gyrA","Ciprofloxacin_R_mutations","Ciprofloxacin_Prediction","Mykrobe_rpsL","Mykrobe_Streptomycin_rrs","Mykrobe_Streptomycin_gid","Streptomycin_R_mutations","Streptomycin_Prediction","Mykrobe_Amikacin_rrs","Amikacin_R_mutations","Amikacin_Prediction","Mykrobe_Capreomycin_rrs","Mykrobe_Capreomycin_tlyA","Capreomycin_R_mutations","Capreomycin_Prediction","Mykrobe_Kanamycin_rrs","Mykrobe_Kanamycin_eis","Kanamycin_R_mutations","Kanamycin_Prediction","Lims_Comment","Lims_INTComment","Mykrobe_Workflow_Version","mykrobe_version","Mykrobe_Resistance_probe_set","Mykrobe_min_depth_default_5","Mykrobe_min_conf_default_10","LIMS_file","Mutation_set_version"
"ERR031480_L6","No Mutation","No Mutation","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""
"ERR125628_MBOV","No Mutation","No Mutation","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","H57D","No Mutation","pncA_H57D-GTG2289071GTC:46:0:5473","R","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""
"ERR181314_L9","No Mutation","No Mutation","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""
"ERR234162_L3","No Mutation","No Mutation","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""
"ERR2659153","No Mutation","No Mutation","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""
"ERR266106_MCAN","No Mutation","No Mutation","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","GCA136GCG","No Mutation","pncA_GCA136GCG-TGC2289104CGC:100:0:12285","R","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""
"ERR2704812_L5","No Mutation","No Mutation","G-48A","No Mutation","No Mutation","ahpC_G-48A-G2726145A:360:0:42983","R","D435V","rpoB_D435V-GAC761109GTC:344:0:40497","R","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""
"ERR3335753_L1","No Mutation","No Mutation","No Mutation","No Mutation","No Mutation",NA,"S","L430P","rpoB_L430P-CTG761094CCG:190:5:14588","R","No Mutation","No Mutation",NA,"S","T389TG;G390GG;G391GG","No Mutation","pncA_T389TG-A2288853CA:43:131:1022__pncA_G390GG-C2288852CC:43:130:1055__pncA_G391GG-C2288851CC:43:130:1058","r","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""
"ERR4143897_MPIN","No Mutation","No Mutation","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""
"ERR756348_L7","No Mutation","No Mutation","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""
"ERR841495_L5","No Mutation","No Mutation","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""
"SRR17089001","No Mutation","No Mutation","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""
"SRR1710097_L2","No Mutation","No Mutation","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""
"SRR3500411_MMUN","No Mutation","No Mutation","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""
"SRR9157804","No Mutation","No Mutation","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation","No Mutation",NA,"S","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","No Mutation","No Mutation",NA,"S","","","","v0.10.0","tb-hunt-probe-set-jan-03-2019.fasta.gz","5","10","",""