changed blind_test_input_df to blind_test_df in MultModelsCl

This commit is contained in:
Tanushree Tunstall 2022-06-22 16:42:04 +01:00
parent bc12dbd7c2
commit 0350784d52
114 changed files with 107251 additions and 863011 deletions

View file

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