added ml_functions dir
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c85c965c3e
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30 changed files with 683 additions and 606160 deletions
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@ -1,158 +1,83 @@
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########################################################################
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#70/30
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# 70/30 [WITHOUT OR]
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########################################################################
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=-----------------------------------=
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# All features including AA index
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# [WITH OR]
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=-----------------------------------=
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time ./run_7030.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_7030.txt #d
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time ./run_7030.py -g embB -d ethambutol 2>&1 | tee log_embb_7030.txt
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time ./run_7030.py -g katG -d isoniazid 2>&1 | tee log_katg_7030.txt
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time ./run_7030.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_7030.txt
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time ./run_7030.py -g gid -d streptomycin 2>&1 | tee log_gid_7030.txt
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time ./run_7030.py -g alr -d cycloserine 2>&1 | tee log_alr_7030.txt
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# alr: # ERROR, as expected, too few values!
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# gid: problems
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=-----------------------------------=
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# All features including AA index
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# [WITHOUT OR] **DONE
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# actual data
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#------------------------------------=
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time ./run_7030.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_7030_noOR.txt
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time ./run_7030.py -g embB -d ethambutol 2>&1 | tee log_embb_7030_noOR.txt
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time ./run_7030.py -g katG -d isoniazid 2>&1 | tee log_katg_7030_noOR.txt
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time ./run_7030.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_7030_noOR.txt
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time ./run_7030.py -g gid -d streptomycin 2>&1 | tee log_gid_7030_noOR.txt
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time ./run_7030.py -g alr -d cycloserine 2>&1 | tee log_alr_7030_noOR.txt
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########################################################################
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# 80/20
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########################################################################
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time ./run_7030.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_7030_.txt
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time ./run_7030.py -g embB -d ethambutol 2>&1 | tee log_embb_7030_.txt
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time ./run_7030.py -g katG -d isoniazid 2>&1 | tee log_katg_7030_.txt
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time ./run_7030.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_7030_.txt
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time ./run_7030.py -g gid -d streptomycin 2>&1 | tee log_gid_7030_.txt
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time ./run_7030.py -g alr -d cycloserine 2>&1 | tee log_alr_7030_.txt
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=-----------------------------------=
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# All features including AA index
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# [WITH OR]
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=-----------------------------------=
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time ./run_8020.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_8020.txt
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time ./run_8020.py -g embB -d ethambutol 2>&1 | tee log_embb_8020.txt
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time ./run_8020.py -g katG -d isoniazid 2>&1 | tee log_katg_8020.txt
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time ./run_8020.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_8020.txt
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time ./run_8020.py -g gid -d streptomycin 2>&1 | tee log_gid_8020.txt
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time ./run_8020.py -g alr -d cycloserine 2>&1 | tee log_alr_8020.txt
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=-----------------------------------=
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# All features including AA index
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# [WITHOUT OR] **DONE
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real 0m1.099s
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user 0m1.308s
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sys 0m1.474s
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=-----------------------------------=
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time ./run_8020.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_8020_noOR.txt
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time ./run_8020.py -g embB -d ethambutol 2>&1 | tee log_embb_8020_noOR.txt
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time ./run_8020.py -g katG -d isoniazid 2>&1 | tee log_katg_8020_noOR.txt
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time ./run_8020.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_8020_noOR.txt
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time ./run_8020.py -g gid -d streptomycin 2>&1 | tee log_gid_8020_noOR.txt
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time ./run_8020.py -g alr -d cycloserine 2>&1 | tee log_alr_8020_noOR.txt
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########################################################################
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# SL
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########################################################################
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=-----------------------------------=
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# All features including AA index
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=-----------------------------------=
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=-----------------------------------=
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# All features including AA index
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# [WITHOUT OR]
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=-----------------------------------=
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time ./run_sl.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_sl_noOR.txt
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time ./run_sl.py -g embB -d ethambutol 2>&1 | tee log_embb_sl_noOR.txt
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time ./run_sl.py -g katG -d isoniazid 2>&1 | tee log_katg_sl_noOR.txt
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time ./run_sl.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_sl_noOR.txt
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time ./run_sl.py -g gid -d streptomycin 2>&1 | tee log_gid_sl_noOR.txt
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time ./run_sl.py -g alr -d cycloserine 2>&1 | tee log_alr_sl_noOR.txt
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########################################################################
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########################################################################
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########################################################################
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###################### COMPLETE DATA ##############################
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########################################################################
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########################################################################
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########################################################################
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#70/30
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########################################################################
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=-----------------------------------=
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# All features including AA index
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# [WITHOUT OR]
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# COMPLETE data
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#------------------------------------=
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time ./run_cd_7030.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_cd_7030_noOR.txt
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time ./run_cd_7030.py -g embB -d ethambutol 2>&1 | tee log_embb_cd_7030_noOR.txt
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time ./run_cd_7030.py -g katG -d isoniazid 2>&1 | tee log_katg_cd_7030_noOR.txt
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time ./run_cd_7030.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_cd_7030_noOR.txt
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time ./run_cd_7030.py -g gid -d streptomycin 2>&1 | tee log_gid_cd_7030_noOR.txt
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time ./run_cd_7030.py -g alr -d cycloserine 2>&1 | tee log_alr_cd_7030_noOR.txt
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time ./run_cd_7030.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_cd_7030_.txt
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time ./run_cd_7030.py -g embB -d ethambutol 2>&1 | tee log_embb_cd_7030_.txt
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time ./run_cd_7030.py -g katG -d isoniazid 2>&1 | tee log_katg_cd_7030_.txt
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time ./run_cd_7030.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_cd_7030_.txt
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time ./run_cd_7030.py -g gid -d streptomycin 2>&1 | tee log_gid_cd_7030_.txt
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time ./run_cd_7030.py -g alr -d cycloserine 2>&1 | tee log_alr_cd_7030_.txt
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########################################################################
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# 80/20
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# 80/20 [WITHOUT OR]
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########################################################################
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=-----------------------------------=
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# actual data
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#------------------------------------=
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time ./run_8020.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_8020_.txt
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time ./run_8020.py -g embB -d ethambutol 2>&1 | tee log_embb_8020_.txt
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time ./run_8020.py -g katG -d isoniazid 2>&1 | tee log_katg_8020_.txt
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time ./run_8020.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_8020_.txt
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time ./run_8020.py -g gid -d streptomycin 2>&1 | tee log_gid_8020_.txt
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time ./run_8020.py -g alr -d cycloserine 2>&1 | tee log_alr_8020_.txt
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=-----------------------------------=
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# All features including AA index
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# [WITHOUT OR]
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# COMPLETE data
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#------------------------------------=
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time ./run_cd_8020.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_cd_8020_noOR.txt
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time ./run_cd_8020.py -g embB -d ethambutol 2>&1 | tee log_embb_cd_8020_noOR.txt
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time ./run_cd_8020.py -g katG -d isoniazid 2>&1 | tee log_katg_cd_8020_noOR.txt
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time ./run_cd_8020.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_cd_8020_noOR.txt
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time ./run_cd_8020.py -g gid -d streptomycin 2>&1 | tee log_gid_cd_8020_noOR.txt
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time ./run_cd_8020.py -g alr -d cycloserine 2>&1 | tee log_alr_cd_8020_noOR.txt
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time ./run_cd_8020.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_cd_8020_.txt
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time ./run_cd_8020.py -g embB -d ethambutol 2>&1 | tee log_embb_cd_8020_.txt
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time ./run_cd_8020.py -g katG -d isoniazid 2>&1 | tee log_katg_cd_8020_.txt
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time ./run_cd_8020.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_cd_8020_.txt
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time ./run_cd_8020.py -g gid -d streptomycin 2>&1 | tee log_gid_cd_8020_.txt
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time ./run_cd_8020.py -g alr -d cycloserine 2>&1 | tee log_alr_cd_8020_.txt
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########################################################################
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# SL
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# SL [WITHOUT OR]
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########################################################################
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=-----------------------------------=
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# All features including AA index
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# [WITHOUT OR]
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# actual data
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#------------------------------------=
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time ./run_cd_sl.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_cd_sl_noOR.txt
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time ./run_cd_sl.py -g embB -d ethambutol 2>&1 | tee log_embb_cd_sl_noOR.txt
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time ./run_cd_sl.py -g katG -d isoniazid 2>&1 | tee log_katg_cd_sl_noOR.txt
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time ./run_cd_sl.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_cd_sl_noOR.txt
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time ./run_cd_sl.py -g gid -d streptomycin 2>&1 | tee log_gid_cd_sl_noOR.txt
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time ./run_cd_sl.py -g alr -d cycloserine 2>&1 | tee log_alr_cd_sl_noOR.txt
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time ./run_sl.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_sl_.txt
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time ./run_sl.py -g embB -d ethambutol 2>&1 | tee log_embb_sl_.txt
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time ./run_sl.py -g katG -d isoniazid 2>&1 | tee log_katg_sl_.txt
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time ./run_sl.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_sl_.txt
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time ./run_sl.py -g gid -d streptomycin 2>&1 | tee log_gid_sl_.txt
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time ./run_sl.py -g alr -d cycloserine 2>&1 | tee log_alr_sl_.txt
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=-----------------------------------=
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# COMPLETE data
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#------------------------------------=
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time ./run_cd_sl.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_cd_sl_.txt
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time ./run_cd_sl.py -g embB -d ethambutol 2>&1 | tee log_embb_cd_sl_.txt
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time ./run_cd_sl.py -g katG -d isoniazid 2>&1 | tee log_katg_cd_sl_.txt
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time ./run_cd_sl.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_cd_sl_.txt
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time ./run_cd_sl.py -g gid -d streptomycin 2>&1 | tee log_gid_cd_sl_.txt
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time ./run_cd_sl.py -g alr -d cycloserine 2>&1 | tee log_alr_cd_sl_.txt
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########################################################################
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@ -167,4 +92,4 @@ time ./run_cd_sl.py -g alr -d cycloserine 2>&1 | tee log_alr_cd_sl_noOR.txt
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time ./run_FS.py -g pncA -d pyrazinamide 2>&1 | tee log_FS_pnca_7030.txt
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time ./run_FS_7030.py -g pncA -d pyrazinamide 2>&1 | tee log_FS_pnca_7030_noOR.txt
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time ./run_FS_7030.py -g pncA -d pyrazinamide 2>&1 | tee log_FS_pnca_7030_.txt
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