changed blind_test_input_df to blind_test_df in MultModelsCl
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bc12dbd7c2
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0350784d52
114 changed files with 107251 additions and 863011 deletions
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@ -1,51 +1,18 @@
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==================================
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# UQ run: same as ORIGINAL except
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# Features NOT including AA index, but includes active site annotations
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# Date: 30/05/2022, but reran with from my desktop on 19/05/2022 to capture log and include active_site indication column
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# captures error: 2>$1
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=================================
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./pnca_config.py 2>&1 | tee log_pnca_config.txt
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./embb_config.py 2>&1 | tee log_embb_config.txt
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./gid_config.py 2>&1 | tee log_gid_config.txt
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./katg_config.py 2>&1 | tee log_katg_config.txt
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./rpob_config.py 2>&1 | tee log_rpob_config.txt
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./alr_config.py 2>&1 | tee log_alr_config.txt
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# ERROR, as expected, too few values!
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########################################################################
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=================================
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# Split: ORIGINAL
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# actual values: training set
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# imputed values: blind set
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# All features including AA index
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# Date: 18/05/2022 # reran with minor formatting and log capture
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# captures error: 2>$1
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=================================
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./pnca_orig.py 2>&1 | tee log_pnca_orig.txt
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./embb_orig.py 2>&1 | tee log_embb_orig.txt
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./gid_orig.py 2>&1 | tee log_gid_orig.txt
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./katg_orig.py 2>&1 | tee log_katg_orig.txt
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./rpob_orig.py 2>&1 | tee log_rpob_orig.txt
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./alr_orig.py 2>&1 | tee log_alr_orig.txt # ERROR, as expected, too few values!
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########################################################################
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=================================
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# Split: 70/30
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# All features including AA index
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# Date: 17/05/2022 and 18/05/2022, reran with minor foramtting and log capture
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# Date: 22/06/2022
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# captures error: 2>$1
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# omitted drtype_labels
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=================================
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./pnca_7030.py 2>&1 | tee log_pnca_7030.txt
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./embb_7030.py 2>&1 | tee log_embb_7030.txt
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./gid_7030.py 2>&1 | tee log_gid_7030.txt
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./katg_7030.py 2>&1 | tee log_katg_7030.txt
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./rpob_7030.py 2>&1 | tee log_rpob_7030.txt
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./alr_7030.py 2>&1 | tee log_alr_7030.txt # ERROR, as expected, too few values!
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problems, CT values are non existing except for rouC
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./run_7030.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_7030.txt
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./run_7030.py -g embB -d ethambutol 2>&1 | tee log_embb_7030.txt
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./run_7030.py -g katG -d isoniazid 2>&1 | tee log_katg_7030.txt
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./run_7030.py -g rpoB -d rifampicin 2>&1 | tee log_rpob_7030.txt
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./run_7030.py -g gid -d streptomycin 2>&1 | tee log_gid_7030.txt
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./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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=================================
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@ -54,12 +21,7 @@ problems, CT values are non existing except for rouC
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# Date: 17/05/2022, 18:48
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# captures error: 2>$1
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=================================
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./pnca_8020.py 2>&1 | tee log_pnca_8020.txt
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./embb_8020.py 2>&1 | tee log_embb_8020.txt
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./gid_8020.py 2>&1 | tee log_gid_8020.txt
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./katg_8020.py 2>&1 | tee log_katg_8020.txt
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./rpob_8020.py 2>&1 | tee log_rpob_8020.txt
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./alr_8020.py 2>&1 | tee log_alr_8020.txt # ERROR, as expected, too few values!
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########################################################################
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@ -69,12 +31,7 @@ problems, CT values are non existing except for rouC
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# Date: 17/05/2022, 18:48
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# captures error: 2>$1
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=================================
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./pnca_sl.py 2>&1 | tee log_pnca_sl.txt
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./embb_sl.py 2>&1 | tee log_embb_sl.txt
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./gid_sl.py 2>&1 | tee log_gid_sl.txt
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./katg_sl.py 2>&1 | tee log_katg_sl.txt
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./rpob_sl.py 2>&1 | tee log_rpob_sl.txt
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./alr_sl.py 2>&1 | tee log_alr_sl.txt # ERROR, as expected, too few values!
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########################################################################
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=================================
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@ -85,12 +42,6 @@ problems, CT values are non existing except for rouC
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# Date: 18/05/2022
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# captures error: 2>$1
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=================================
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./pnca_rt.py 2>&1 | tee log_pnca_rt.txt
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./embb_rt.py 2>&1 | tee log_embb_rt.txt
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./gid_rt.py 2>&1 | tee log_gid_rt.txt
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./katg_rt.py 2>&1 | tee log_katg_rt.txt
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./rpob_rt.py 2>&1 | tee log_rpob_rt.txt
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./alr_rt.py 2>&1 | tee log_alr_rt.txt # ERROR, as expected, too few values!
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########################################################################
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# COMPLETE Data: actual + na i.e imputed
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@ -102,12 +53,7 @@ problems, CT values are non existing except for rouC
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# Date: 18/05/2022
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# captures error: 2>$1
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=================================
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./pnca_cd_7030.py 2>&1 | tee log_pnca_cd_7030.txt
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./embb_cd_7030.py 2>&1 | tee log_embb_cd_7030.txt
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./gid_cd_7030.py 2>&1 | tee log_gid_cd_7030.txt
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./katg_cd_7030.py 2>&1 | tee log_katg_cd_7030.txt
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./rpob_cd_7030.py 2>&1 | tee log_rpob_cd_7030.txt
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./alr_cd_7030.py 2>&1 | tee log_alr_cd_7030.txt # ERROR, as expected, too few values!
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########################################################################
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=================================
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@ -116,12 +62,6 @@ problems, CT values are non existing except for rouC
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# Date: 18/05/2022
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# captures error: 2>$1
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=================================
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./pnca_cd_8020.py 2>&1 | tee log_pnca_cd_8020.txt
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./embb_cd_8020.py 2>&1 | tee log_embb_cd_8020.txt
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./gid_cd_8020.py 2>&1 | tee log_gid_cd_8020.txt
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./katg_cd_8020.py 2>&1 | tee log_katg_cd_8020.txt
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./rpob_cd_8020.py 2>&1 | tee log_rpob_cd_8020.txt
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./alr_cd_8020.py 2>&1 | tee log_alr_cd_8020.txt # ERROR, as expected, too few values!
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=================================
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# Split: scaling law [COMPLETE DATA]
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@ -129,10 +69,5 @@ problems, CT values are non existing except for rouC
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# Date: 18/05/2022
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# captures error: 2>$1
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=================================
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./pnca_cd_sl.py 2>&1 | tee log_pnca_cd_sl.txt
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./embb_cd_sl.py 2>&1 | tee log_embb_cd_sl.txt
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./gid_cd_sl.py 2>&1 | tee log_gid_cd_sl.txt
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./katg_cd_sl.py 2>&1 | tee log_katg_cd_sl.txt
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./rpob_cd_sl.py 2>&1 | tee log_rpob_cd_sl.txt
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./alr_cd_sl.py 2>&1 | tee log_alr_cd_sl.txt # ERROR, as expected, too few values!
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