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iqbal-lab / Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop
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Pulling m2 into master #103

Closed Phelimb closed 8 years ago

Phelimb commented 8 years ago

Making an issue instead of a PR as the branches don't share commit history so we won't be able to pull via github.

@iqbal-lab I think m2 is stable enough now to be merged into master. Below are the comparisons of the AMR prediction results on the full sets from the NCOMMS paper for staph and TB. There are a few minor changes - mostly an increase in specificity in m2 with no loss in sensitivity.

I've also included a comparison of the walker panel with that from the original panel as this is new in m2 also.

TB

Ana1 - f943547e7cfb965bc0c6aa24934778765a9d188a (master)

Drug Total FN(R) FP(S) VME ME sensitivity specificity PPV NPV
----- ----- ----- ----- ----- ----- ----- ----- ----- -----
Rifampicin 2971 23 (371) 23 (2600) 6.2% (4.2%-9.1%) 0.9% (0.6%-1.3%) 93.8% (90.9%-95.8%) 99.1% (98.7%-99.4%) 93.8% (90.9%-95.8%) 99.1% (98.7%-99.4%)
Capreomycin 326 7 (56) 14 (270) 12.5% (6.2%-23.6%) 5.2% (3.1%-8.5%) 87.5% (76.4%-93.8%) 94.8% (91.5%-96.9%) 77.8% (66.1%-86.3%) 97.3% (94.6%-98.7%)
all 11881 259 (1753) 176 (10128) 14.8% (13.2%-16.5%) 1.7% (1.5%-2.0%) 85.2% (83.5%-86.8%) 98.3% (98.0%-98.5%) 89.5% (87.9%-90.8%) 97.5% (97.1%-97.8%)
Isoniazid 3011 68 (586) 23 (2425) 11.6% (9.3%-14.4%) 0.9% (0.6%-1.4%) 88.4% (85.6%-90.7%) 99.1% (98.6%-99.4%) 95.7% (93.7%-97.2%) 97.2% (96.5%-97.8%)
Amikacin 330 5 (62) 6 (268) 8.1% (3.5%-17.5%) 2.2% (1.0%-4.8%) 91.9% (82.5%-96.5%) 97.8% (95.2%-99.0%) 90.5% (80.7%-95.6%) 98.1% (95.7%-99.2%)
Ethambutol 2987 56 (238) 94 (2749) 23.5% (18.6%-29.3%) 3.4% (2.8%-4.2%) 76.5% (70.7%-81.4%) 96.6% (95.8%-97.2%) 65.9% (60.2%-71.3%) 97.9% (97.3%-98.4%)
Kanamycin 106 4 (11) 1 (95) 36.4% (15.2%-64.6%) 1.1% (0.2%-5.7%) 63.6% (35.4%-84.8%) 98.9% (94.3%-99.8%) 87.5% (52.9%-97.8%) 95.9% (90.0%-98.4%)
Streptomycin 1579 90 (394) 9 (1185) 22.8% (19.0%-27.2%) 0.8% (0.4%-1.4%) 77.2% (72.8%-81.0%) 99.2% (98.6%-99.6%) 97.1% (94.6%-98.5%) 92.9% (91.3%-94.2%)
Quinolones 571 6 (35) 6 (536) 17.1% (8.1%-32.7%) 1.1% (0.5%-2.4%) 82.9% (67.3%-91.9%) 98.9% (97.6%-99.5%) 82.9% (67.3%-91.9%) 98.9% (97.6%-99.5%)

Ana2 - 0e9e70d295250bb1c7ecfd4a31c1100d17311d21 - m2

Drug Total FN(R) FP(S) VME ME sensitivity specificity PPV NPV
Rifampicin 2971 19 (371) 20 (2600) 5.1% (3.3%-7.9%) 0.8% (0.5%-1.2%) 94.9% (92.1%-96.7%) 99.2% (98.8%-99.5%) 94.6% (91.8%-96.5%) 99.3% (98.9%-99.5%)
Capreomycin 326 6 (56) 12 (270) 10.7% (5.0%-21.5%) 4.4% (2.6%-7.6%) 89.3% (78.5%-95.0%) 95.6% (92.4%-97.4%) 80.6% (69.2%-88.6%) 97.7% (95.1%-99.0%)
all 11881 233 (1753) 166 (10128) 13.3% (11.8%-15.0%) 1.6% (1.4%-1.9%) 86.7% (85.0%-88.2%) 98.4% (98.1%-98.6%) 90.2% (88.6%-91.5%) 97.7% (97.4%-98.0%)
Isoniazid 3011 65 (586) 21 (2425) 11.1% (8.8%-13.9%) 0.9% (0.6%-1.3%) 88.9% (86.1%-91.2%) 99.1% (98.7%-99.4%) 96.1% (94.2%-97.5%) 97.4% (96.7%-97.9%)
Amikacin 330 4 (62) 4 (268) 6.5% (2.5%-15.4%) 1.5% (0.6%-3.8%) 93.5% (84.6%-97.5%) 98.5% (96.2%-99.4%) 93.5% (84.6%-97.5%) 98.5% (96.2%-99.4%)
Ethambutol 2987 55 (238) 93 (2749) 23.1% (18.2%-28.9%) 3.4% (2.8%-4.1%) 76.9% (71.1%-81.8%) 96.6% (95.9%-97.2%) 66.3% (60.5%-71.6%) 98.0% (97.4%-98.4%)
Kanamycin 106 0 (11) 0 (95) 0.0% (0.0%-25.9%) 0.0% (0.0%-3.9%) 100.0% (74.1%-100.0%) 100.0% (96.1%-100.0%) 100.0% (74.1%-100.0%) 100.0% (96.1%-100.0%)
Streptomycin 1579 78 (394) 10 (1185) 19.8% (16.2%-24.0%) 0.8% (0.5%-1.5%) 80.2% (76.0%-83.8%) 99.2% (98.5%-99.5%) 96.9% (94.4%-98.3%) 93.8% (92.3%-95.0%)
Quinolones 571 6 (35) 6 (536) 17.1% (8.1%-32.7%) 1.1% (0.5%-2.4%) 82.9% (67.3%-91.9%) 98.9% (97.6%-99.5%) 82.9% (67.3%-91.9%) 98.9% (97.6%-99.5%)

diff ana2 - ana1

Drug Total (+/-) TP (+/-) FP (+/-) TN (+/-) FN (+/-) sensitivity (+/-) specificity (+/-)
Rifampicin +0.000000 +4.000000 -3.000000 +3.000000 -4.000000 +1.100000 +0.100000
Capreomycin +0.000000 +1.000000 -2.000000 +2.000000 -1.000000 +1.800000 +0.800000
all +0.000000 +26.000000 -10.000000 +10.000000 -26.000000 +1.500000 +0.100000
Isoniazid +0.000000 +3.000000 -2.000000 +2.000000 -3.000000 +0.500000 +0.000000
Amikacin +0.000000 +1.000000 -2.000000 +2.000000 -1.000000 +1.600000 +0.700000
Ethambutol +0.000000 +1.000000 -1.000000 +1.000000 -1.000000 +0.400000 +0.000000
Kanamycin +0.000000 +4.000000 -1.000000 +1.000000 -4.000000 +36.400000 +1.100000
Streptomycin +0.000000 +12.000000 +1.000000 -1.000000 -12.000000 +3.000000 +0.000000
Quinolones +0.000000 +0.000000 +0.000000 +0.000000 +0.000000 +0.000000 +0.000000

Staph

compare master 4c8dc62f435c686d39bdf3ba29bdf980317fda71 vs d3c269b5c4a639d219cee9215835126301c2d6b1 (m2)

./scripts/compare.py --analysis summary --markdown /data2/users/phelim/ana/staph/mykrobe/pheno/comid_to_combined_truth.json --ana1 /data2/users/phelim/ana/staph/atlas/amr/4c8dc62f435c686d39bdf3ba29bdf980317fda71/C000*.json --ana2 /data2/users/phelim/ana/staph/atlas/amr/d3c269b5c4a639d219cee9215835126301c2d6b1/C000*.json > summary_compare_staph_4c8dc62f43_d3c269b5c4a.txt

Ana1

Drug Total FN(R) FP(S) VME ME sensitivity specificity PPV NPV
----- ----- ----- ----- ----- ----- ----- ----- ----- -----
Rifampicin 1029 1 (10) 1 (1019) 10.0% (1.8%-40.4%) 0.1% (0.0%-0.6%) 90.0% (59.6%-98.2%) 99.9% (99.4%-100.0%) 90.0% (59.6%-98.2%) 99.9% (99.4%-100.0%)
Clindamycin 1029 2 (178) 9 (851) 1.1% (0.3%-4.0%) 1.1% (0.6%-2.0%) 98.9% (96.0%-99.7%) 98.9% (98.0%-99.4%) 95.1% (91.0%-97.4%) 99.8% (99.1%-99.9%)
all 12309 38 (2042) 70 (10267) 1.9% (1.4%-2.5%) 0.7% (0.5%-0.9%) 98.1% (97.5%-98.6%) 99.3% (99.1%-99.5%) 96.6% (95.8%-97.3%) 99.6% (99.5%-99.7%)
Vancomycin 1029 0 (2) 0 (1027) 0.0% (0.0%-65.7%) 0.0% (0.0%-0.4%) 100.0% (34.3%-100.0%) 100.0% (99.6%-100.0%) 100.0% (34.3%-100.0%) 100.0% (99.6%-100.0%)
Methicillin 1029 3 (218) 5 (811) 1.4% (0.5%-4.0%) 0.6% (0.3%-1.4%) 98.6% (96.0%-99.5%) 99.4% (98.6%-99.7%) 97.7% (94.8%-99.0%) 99.6% (98.9%-99.9%)
Mupirocin 1029 0 (53) 6 (976) 0.0% (0.0%-6.8%) 0.6% (0.3%-1.3%) 100.0% (93.2%-100.0%) 99.4% (98.7%-99.7%) 89.8% (79.5%-95.3%) 100.0% (99.6%-100.0%)
Trimethoprim 1029 5 (62) 5 (967) 8.1% (3.5%-17.5%) 0.5% (0.2%-1.2%) 91.9% (82.5%-96.5%) 99.5% (98.8%-99.8%) 91.9% (82.5%-96.5%) 99.5% (98.8%-99.8%)
Ciprofloxacin 1029 14 (244) 9 (785) 5.7% (3.4%-9.4%) 1.1% (0.6%-2.2%) 94.3% (90.6%-96.6%) 98.9% (97.8%-99.4%) 96.2% (93.0%-98.0%) 98.2% (97.0%-98.9%)
Penicillin 1029 5 (838) 13 (191) 0.6% (0.3%-1.4%) 6.8% (4.0%-11.3%) 99.4% (98.6%-99.7%) 93.2% (88.7%-96.0%) 98.5% (97.4%-99.1%) 97.3% (93.8%-98.8%)
Tetracycline 1029 0 (48) 3 (981) 0.0% (0.0%-7.4%) 0.3% (0.1%-0.9%) 100.0% (92.6%-100.0%) 99.7% (99.1%-99.9%) 94.1% (84.1%-98.0%) 100.0% (99.6%-100.0%)
Erythromycin 1029 4 (219) 3 (810) 1.8% (0.7%-4.6%) 0.4% (0.1%-1.1%) 98.2% (95.4%-99.3%) 99.6% (98.9%-99.9%) 98.6% (96.0%-99.5%) 99.5% (98.7%-99.8%)
FusidicAcid 2019 4 (170) 16 (1849) 2.4% (0.9%-5.9%) 0.9% (0.5%-1.4%) 97.6% (94.1%-99.1%) 99.1% (98.6%-99.5%) 91.2% (86.2%-94.5%) 99.8% (99.4%-99.9%)

Ana2

Drug Total FN(R) FP(S) VME ME sensitivity specificity PPV NPV
Rifampicin 1029 1 (10) 1 (1019) 10.0% (1.8%-40.4%) 0.1% (0.0%-0.6%) 90.0% (59.6%-98.2%) 99.9% (99.4%-100.0%) 90.0% (59.6%-98.2%) 99.9% (99.4%-100.0%)
Clindamycin 1029 2 (178) 7 (851) 1.1% (0.3%-4.0%) 0.8% (0.4%-1.7%) 98.9% (96.0%-99.7%) 99.2% (98.3%-99.6%) 96.2% (92.3%-98.1%) 99.8% (99.1%-99.9%)
all 12309 38 (2042) 60 (10267) 1.9% (1.4%-2.5%) 0.6% (0.5%-0.8%) 98.1% (97.5%-98.6%) 99.4% (99.2%-99.5%) 97.1% (96.3%-97.7%) 99.6% (99.5%-99.7%)
Vancomycin 1029 0 (2) 0 (1027) 0.0% (0.0%-65.7%) 0.0% (0.0%-0.4%) 100.0% (34.3%-100.0%) 100.0% (99.6%-100.0%) 100.0% (34.3%-100.0%) 100.0% (99.6%-100.0%)
Methicillin 1029 3 (218) 5 (811) 1.4% (0.5%-4.0%) 0.6% (0.3%-1.4%) 98.6% (96.0%-99.5%) 99.4% (98.6%-99.7%) 97.7% (94.8%-99.0%) 99.6% (98.9%-99.9%)
Mupirocin 1029 0 (53) 4 (976) 0.0% (0.0%-6.8%) 0.4% (0.2%-1.0%) 100.0% (93.2%-100.0%) 99.6% (99.0%-99.8%) 93.0% (83.3%-97.2%) 100.0% (99.6%-100.0%)
Trimethoprim 1029 5 (62) 4 (967) 8.1% (3.5%-17.5%) 0.4% (0.2%-1.1%) 91.9% (82.5%-96.5%) 99.6% (98.9%-99.8%) 93.4% (84.3%-97.4%) 99.5% (98.8%-99.8%)
Ciprofloxacin 1029 14 (244) 8 (785) 5.7% (3.4%-9.4%) 1.0% (0.5%-2.0%) 94.3% (90.6%-96.6%) 99.0% (98.0%-99.5%) 96.6% (93.5%-98.3%) 98.2% (97.1%-98.9%)
Penicillin 1029 5 (838) 12 (191) 0.6% (0.3%-1.4%) 6.3% (3.6%-10.7%) 99.4% (98.6%-99.7%) 93.7% (89.3%-96.4%) 98.6% (97.5%-99.2%) 97.3% (93.8%-98.8%)
Tetracycline 1029 0 (48) 4 (981) 0.0% (0.0%-7.4%) 0.4% (0.2%-1.0%) 100.0% (92.6%-100.0%) 99.6% (99.0%-99.8%) 92.3% (81.8%-97.0%) 100.0% (99.6%-100.0%)
Erythromycin 1029 4 (219) 3 (810) 1.8% (0.7%-4.6%) 0.4% (0.1%-1.1%) 98.2% (95.4%-99.3%) 99.6% (98.9%-99.9%) 98.6% (96.0%-99.5%) 99.5% (98.7%-99.8%)
FusidicAcid 2019 4 (170) 12 (1849) 2.4% (0.9%-5.9%) 0.6% (0.4%-1.1%) 97.6% (94.1%-99.1%) 99.4% (98.9%-99.6%) 93.3% (88.6%-96.1%) 99.8% (99.4%-99.9%)

diff ana2 - ana1

Drug Total (+/-) TP (+/-) FP (+/-) TN (+/-) FN (+/-) sensitivity (+/-) specificity (+/-)
Rifampicin +0.000000 +0.000000 +0.000000 +0.000000 +0.000000 +0.000000 +0.000000
Clindamycin +0.000000 +0.000000 -2.000000 +2.000000 +0.000000 +0.000000 +0.300000
all +0.000000 +0.000000 -10.000000 +10.000000 +0.000000 +0.000000 +0.100000
Vancomycin +0.000000 +0.000000 +0.000000 +0.000000 +0.000000 +0.000000 +0.000000
Methicillin +0.000000 +0.000000 +0.000000 +0.000000 +0.000000 +0.000000 +0.000000
Mupirocin +0.000000 +0.000000 -2.000000 +2.000000 +0.000000 +0.000000 +0.200000
Trimethoprim +0.000000 +0.000000 -1.000000 +1.000000 +0.000000 +0.000000 +0.100000
Ciprofloxacin +0.000000 +0.000000 -1.000000 +1.000000 +0.000000 +0.000000 +0.100000
Penicillin +0.000000 +0.000000 -1.000000 +1.000000 +0.000000 +0.000000 +0.500000
Tetracycline +0.000000 +0.000000 +1.000000 -1.000000 +0.000000 +0.000000 -0.100000
Erythromycin +0.000000 +0.000000 +0.000000 +0.000000 +0.000000 +0.000000 +0.000000
FusidicAcid +0.000000 +0.000000 -4.000000 +4.000000 +0.000000 +0.000000 +0.300000 
./scripts/compare.py --analysis diff --markdown /data2/users/phelim/ana/staph/mykrobe/pheno/comid_to_combined_truth.json --ana1 /data2/users/phelim/ana/staph/atlas/amr/4c8dc62f435c686d39bdf3ba29bdf980317fda71/C000*.json --ana2 /data2/users/phelim/ana/staph/atlas/amr/d3c269b5c4a639d219cee9215835126301c2d6b1/C000*.json > diff_compare_staph_4c8dc62f43_d3c269b5c4a.txt
sample drug truth ana1 ana2
C00001446 Ciprofloxacin S R S
C00012813 Ciprofloxacin S S R
C00003248 Ciprofloxacin S S R
C00002655 Ciprofloxacin S R S
C00001249 Ciprofloxacin S S R
C00003397 Ciprofloxacin S S R
C00001215 Ciprofloxacin S R S
C00007091 Ciprofloxacin S R S
C00003099 Penicillin S r S
C00003385 Tetracycline S S r
C00013239 Ciprofloxacin S R S
C00013344 FusidicAcid S r S
C00003226 FusidicAcid S R S

Walker-2015 panel (TB) new in M2

compare 8776690f00eb8c404363ae506e765937df4b3fb9 bradley with walker

./scripts/compare.py --markdown /data2/users/phelim/ana/tb/mykrobe/pheno/comid_to_combined_truth.json  --ana1 /data2/users/phelim/ana/tb/atlas/amr/8776690f00eb8c404363ae506e765937df4b3fb9/bradley-2015/*.json --ana2 /data2/users/phelim/ana/tb/atlas/amr/8776690f00eb8c404363ae506e765937df4b3fb9/walker-2015/*.json  > summary_compare_8776690f0_bradley_walker.txt

Ana1 - ncomms catalog

Drug Total FN(R) FP(S) VME ME sensitivity specificity PPV NPV
----- ----- ----- ----- ----- ----- ----- ----- ----- -----
Rifampicin 2971 19 (371) 20 (2600) 5.1% (3.3%-7.9%) 0.8% (0.5%-1.2%) 94.9% (92.1%-96.7%) 99.2% (98.8%-99.5%) 94.6% (91.8%-96.5%) 99.3% (98.9%-99.5%)
Capreomycin 326 6 (56) 12 (270) 10.7% (5.0%-21.5%) 4.4% (2.6%-7.6%) 89.3% (78.5%-95.0%) 95.6% (92.4%-97.4%) 80.6% (69.2%-88.6%) 97.7% (95.1%-99.0%)
all 14843 411 (1968) 169 (12875) 20.9% (19.1%-22.7%) 1.3% (1.1%-1.5%) 79.1% (77.3%-80.9%) 98.7% (98.5%-98.9%) 90.2% (88.7%-91.5%) 96.9% (96.6%-97.2%)
Isoniazid 3013 65 (586) 21 (2427) 11.1% (8.8%-13.9%) 0.9% (0.6%-1.3%) 88.9% (86.1%-91.2%) 99.1% (98.7%-99.4%) 96.1% (94.2%-97.5%) 97.4% (96.7%-97.9%)
Amikacin 330 4 (62) 4 (268) 6.5% (2.5%-15.4%) 1.5% (0.6%-3.8%) 93.5% (84.6%-97.5%) 98.5% (96.2%-99.4%) 93.5% (84.6%-97.5%) 98.5% (96.2%-99.4%)
Pyrazinamide 2957 177 (214) 3 (2743) 82.7% (77.1%-87.2%) 0.1% (0.0%-0.3%) 17.3% (12.8%-22.9%) 99.9% (99.7%-100.0%) 92.5% (80.1%-97.4%) 93.9% (93.0%-94.7%)
Ethambutol 2990 56 (239) 93 (2751) 23.4% (18.5%-29.2%) 3.4% (2.8%-4.1%) 76.6% (70.8%-81.5%) 96.6% (95.9%-97.2%) 66.3% (60.5%-71.6%) 97.9% (97.3%-98.4%)
Kanamycin 106 0 (11) 0 (95) 0.0% (0.0%-25.9%) 0.0% (0.0%-3.9%) 100.0% (74.1%-100.0%) 100.0% (96.1%-100.0%) 100.0% (74.1%-100.0%) 100.0% (96.1%-100.0%)
Streptomycin 1579 78 (394) 10 (1185) 19.8% (16.2%-24.0%) 0.8% (0.5%-1.5%) 80.2% (76.0%-83.8%) 99.2% (98.5%-99.5%) 96.9% (94.4%-98.3%) 93.8% (92.3%-95.0%)
Quinolones 571 6 (35) 6 (536) 17.1% (8.1%-32.7%) 1.1% (0.5%-2.4%) 82.9% (67.3%-91.9%) 98.9% (97.6%-99.5%) 82.9% (67.3%-91.9%) 98.9% (97.6%-99.5%)

Ana2 - walker catalog

Drug Total FN(R) FP(S) VME ME sensitivity specificity PPV NPV
Rifampicin 2970 12 (371) 40 (2599) 3.2% (1.9%-5.6%) 1.5% (1.1%-2.1%) 96.8% (94.4%-98.1%) 98.5% (97.9%-98.9%) 90.0% (86.6%-92.6%) 99.5% (99.2%-99.7%)
Capreomycin 326 5 (56) 15 (270) 8.9% (3.9%-19.2%) 5.6% (3.4%-9.0%) 91.1% (80.8%-96.1%) 94.4% (91.0%-96.6%) 77.3% (65.8%-85.7%) 98.1% (95.6%-99.2%)
all 14839 170 (1968) 279 (12871) 8.6% (7.5%-10.0%) 2.2% (1.9%-2.4%) 91.4% (90.0%-92.5%) 97.8% (97.6%-98.1%) 86.6% (85.0%-88.0%) 98.7% (98.5%-98.9%)
Isoniazid 3012 41 (586) 24 (2426) 7.0% (5.2%-9.4%) 1.0% (0.7%-1.5%) 93.0% (90.6%-94.8%) 99.0% (98.5%-99.3%) 95.8% (93.8%-97.1%) 98.3% (97.7%-98.8%)
Amikacin 330 4 (62) 4 (268) 6.5% (2.5%-15.4%) 1.5% (0.6%-3.8%) 93.5% (84.6%-97.5%) 98.5% (96.2%-99.4%) 93.5% (84.6%-97.5%) 98.5% (96.2%-99.4%)
Pyrazinamide 2956 51 (214) 50 (2742) 23.8% (18.6%-30.0%) 1.8% (1.4%-2.4%) 76.2% (70.0%-81.4%) 98.2% (97.6%-98.6%) 76.5% (70.4%-81.7%) 98.1% (97.6%-98.6%)
Ethambutol 2989 20 (239) 121 (2750) 8.4% (5.5%-12.6%) 4.4% (3.7%-5.2%) 91.6% (87.4%-94.5%) 95.6% (94.8%-96.3%) 64.4% (59.2%-69.3%) 99.2% (98.8%-99.5%)
Kanamycin 106 0 (11) 0 (95) 0.0% (0.0%-25.9%) 0.0% (0.0%-3.9%) 100.0% (74.1%-100.0%) 100.0% (96.1%-100.0%) 100.0% (74.1%-100.0%) 100.0% (96.1%-100.0%)
Streptomycin 1579 33 (394) 19 (1185) 8.4% (6.0%-11.5%) 1.6% (1.0%-2.5%) 91.6% (88.5%-94.0%) 98.4% (97.5%-99.0%) 95.0% (92.3%-96.8%) 97.2% (96.2%-98.0%)
Quinolones 571 4 (35) 6 (536) 11.4% (4.5%-25.9%) 1.1% (0.5%-2.4%) 88.6% (74.1%-95.5%) 98.9% (97.6%-99.5%) 83.8% (68.9%-92.3%) 99.3% (98.1%-99.7%)

diff ana2 - ana1

Drug Total (+/-) TP (+/-) FP (+/-) TN (+/-) FN (+/-) sensitivity (+/-) specificity (+/-)
Rifampicin -1.000000 +7.000000 +20.000000 -21.000000 -7.000000 +1.900000 -0.700000
Capreomycin +0.000000 +1.000000 +3.000000 -3.000000 -1.000000 +1.800000 -1.200000
all -4.000000 +241.000000 +110.000000 -114.000000 -241.000000 +12.300000 -0.900000
Isoniazid -1.000000 +24.000000 +3.000000 -4.000000 -24.000000 +4.100000 -0.100000
Amikacin +0.000000 +0.000000 +0.000000 +0.000000 +0.000000 +0.000000 +0.000000
Pyrazinamide -1.000000 +126.000000 +47.000000 -48.000000 -126.000000 +58.900000 -1.700000
Ethambutol -1.000000 +36.000000 +28.000000 -29.000000 -36.000000 +15.000000 -1.000000
Kanamycin +0.000000 +0.000000 +0.000000 +0.000000 +0.000000 +0.000000 +0.000000
Streptomycin +0.000000 +45.000000 +9.000000 -9.000000 -45.000000 +11.400000 -0.800000
Quinolones +0.000000 +2.000000 +0.000000 +0.000000 -2.000000 +5.700000 +0.000000
iqbal-lab commented 8 years ago

Accepted - go ahead and merge