added FS to MultClfs.py and modified data for different splits for consistency
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e2bc384155
12 changed files with 1585 additions and 994 deletions
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@ -1,11 +1,13 @@
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=================================
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# Split: 70/30
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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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# 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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time ./run_7030.py -g pncA -d pyrazinamide 2>&1 | tee log_pnca_7030.txt
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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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@ -14,71 +16,155 @@ 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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=================================
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# Split: 80/20
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=-----------------------------------=
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# All features including AA index
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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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# [WITHOUT OR] **DONE
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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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=================================
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# Split: scaling law
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=-----------------------------------=
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# All features including AA index
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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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# [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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=================================
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# Split: REVERSE training
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# imputed values: training set
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# actual values: blind set
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=-----------------------------------=
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# All features including AA index
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# Date: 18/05/2022
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# captures error: 2>$1
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=================================
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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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# COMPLETE Data: actual + na i.e imputed
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# SL
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########################################################################
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=================================
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# Split: 70/30 [COMPLETE DATA]
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=-----------------------------------=
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# All features including AA index
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# Date: 18/05/2022
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# captures error: 2>$1
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=================================
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=-----------------------------------=
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########################################################################
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=================================
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# Split: 80/20 [COMPLETE DATA]
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=-----------------------------------=
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# All features including AA index
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# Date: 18/05/2022
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# captures error: 2>$1
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=================================
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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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# Split: scaling law [COMPLETE DATA]
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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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# Date: 18/05/2022
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# captures error: 2>$1
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=================================
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# [WITHOUT OR]
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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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########################################################################
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# 80/20
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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_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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########################################################################
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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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# [WITHOUT OR]
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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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########################################################################
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########################################################################
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########################################################################
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###################### Feature Selection ##########################
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########################################################################
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########################################################################
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# running feature selection
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# Split:70/30
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# 7030
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time ./run_FS.py -g pncA -d pyrazinamide 2>&1 | tee log_FS_pnca_7030.txt
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real 338m26.705s
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user 1946m12.173s
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sys 189m40.122s
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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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