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maincleaniter.sh
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#!/bin/sh
#SBATCH --job-name=maiter_R_tainn
#SBATCH --time=10:50:00
#SBATCH --mem=200Gb
#SBATCH --cpus-per-task=8
#SBATCH --partition=workq
#SBATCH -e maiter_R_tainn.%J.err
#SBATCH -o maiter_R_tainn.%J.out
python mainclean_interation_v1ecoli.py --input_file $1 --cleanfile $2 --file_type 5 --reward 1 --iter 10 --cpu 4 --gram $3 --name $4 --threshold 8 --media $5
python mainclean_interation_v2.py \
--input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta \
--cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl \
--file_type 7 --reward 0.1 --iter 10 --cpu 8 --gram negative --block_flage 0 --flux_flage 0 --name iLJ478_allec
# media="'cpd00001_e','cpd00007_e','cpd00009_e','cpd00013_e','cpd00018_e','cpd00023_e','cpd00027_e','cpd00028_e','cpd00030_e','cpd00033_e','cpd00034_e','cpd00035_e','cpd00039_e','cpd00041_e','cpd00046_e','cpd00048_e','cpd00051_e','cpd00054_e','cpd00058_e','cpd00060_e','cpd00063_e','cpd00065_e','cpd00066_e','cpd00067_e','cpd00069_e','cpd00091_e','cpd00092_e','cpd00099_e','cpd00107_e','cpd00119_e','cpd00126_e','cpd00129_e','cpd00149_e','cpd00156_e','cpd00161_e','cpd00182_e','cpd00184_e','cpd00205_e','cpd00215_e','cpd00218_e','cpd00220_e','cpd00226_e','cpd00239_e','cpd00244_e','cpd00246_e','cpd00249_e','cpd00254_e','cpd00311_e','cpd00322_e','cpd00381_e','cpd00393_e','cpd00438_e','cpd00531_e','cpd00541_e','cpd00644_e','cpd00654_e','cpd00793_e','cpd00971_e','cpd01012_e','cpd01048_e','cpd03424_e','cpd10515_e','cpd10516_e','cpd11574_e','cpd09695_e'"
# echo media: $media
# python mainclean_interation_v1ecoli.py --input_file $1 --cleanfile $2 --file_type 5 --reward 1 --iter 10 --cpu 4 --gram $3 --name $4 --threshold 0.8 --media $media
# python mainclean_interation_v1ecoli.py --input_file $1 --cleanfile $2 --file_type 5 --reward 0.1 --iter 10 --cpu 4 --gram $3 --name $4 --threshold 0.3
# python mainclean_interation_v1ecoli.py --input_file $1 --cleanfile $2 --file_type 5 --reward 0.1 --iter 10 --cpu 4 --gram $3 --name $4 --threshold 0.5
# python mainclean_interation_v1ecoli_conti.py --input_file $1 --cleanfile $2 --file_type 5 --reward 0.1 --iter 10 --cpu 4 --gram $3 --name $4 --threshold 0.3 --conti $5
# python mainclean_interation_v1ecoli_conti.py --input_file $1 --cleanfile $2 --file_type 5 --reward 0.1 --iter 10 --cpu 4 --gram $3 --name $4 --threshold 0.5 --conti $5
# echo try for iaf987 reverse
# python mainclean_interation_v0.py --input_file /ibex/user/niuk0a/funcarve/cobra/aaseq_CP000148.1.fasta --cleanfile /ibex/user/niuk0a/funcarve/cobra/aaseq_CP000148.1_maxsep.csv --file_type 5 --reward 0.1 --iter 10 --cpu 8 --gram negative --name iaf987INTER_RR5
# echo for ecoli reverse
# python mainclean_interation_v1ecoli.py --input_file /ibex/user/niuk0a/funcarve/cobra/NC_000913.3_ecoli.fasta --cleanfile /ibex/user/niuk0a/funcarve/cobra/NC_000913.3_ecoli_maxsep.csv --file_type 5 --reward 0.1 --iter 10 --cpu 4 --gram negative --name ecoliINTER1_RR5
# echo for
# iLJ478 NC_000853.1 243274 Thermotoga maritima MSB8 243274 negative
# iJN678 BA000022.2 1148 Synechocystis sp. PCC 6803 1148 negative
# iJN1463 NC_002947.4 160488 Pseudomonas putida KT2440 160488 negative
# iCN900 AM180355.1 272563 Clostridioides difficile 630 272563 postive
# iHN637 NC_014328.1 748727 Clostridium ljungdahlii DSM 13528 748727 postive
# iAF1260 NC_000913.3 511145/83333 Escherichia coli str. K-12 substr. MG1655 511145 negative
# iAF987 CP000148.1 269799 Geobacter metallireducens GS-15 269799 negative
# iCN718 NC_010410.1 509173 Acinetobacter baumannii AYE 509173 negative
# NOT USEFUL FROM NOW ON echo for iLJ478 reverse
# python mainclean_interation_v0.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_maxsep.csv --file_type 5 --reward 0.1 --iter 10 --cpu 8 --gram negative --name iLJ478_R
# echo for iJN678 reverse
# python mainclean_interation_v0.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/BA000022.2.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/BA000022.2_maxsep.csv --file_type 5 --reward 0.1 --iter 10 --cpu 8 --gram negative --name iJN678_R_test
# echo for iJN1463 reverse
# python mainclean_interation_v0.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_002947.4.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_002947.4_maxsep.csv --file_type 5 --reward 0.1 --iter 10 --cpu 8 --gram negative --name iJN1463_R
# echo for iCN900 reverse
# python mainclean_interation_v0.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_maxsep.csv --file_type 5 --reward 0.1 --iter 10 --cpu 8 --gram positive --name iCN900_R
# echo for iHN637 reverse
# python mainclean_interation_v0.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_014328.1.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_014328.1_maxsep.csv --file_type 5 --reward 0.1 --iter 10 --cpu 8 --gram positive --name iHN637_R
# echo for iAF1260 reverse
# python mainclean_interation_v0.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000913.3.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000913.3_maxsep.csv --file_type 5 --reward 0.1 --iter 10 --cpu 8 --gram negative --name iAF1260_R
# echo for iCN718 reverse
# python mainclean_interation_v0.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_010410.1.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_010410.1_maxsep.csv --file_type 5 --reward 0.1 --iter 10 --cpu 8 --gram negative --name iCN718_R
# echo done all reverse
# wait for clean result finished run
# 9 iNJ661 NC_000962.3 83332 Mycobacterium tuberculosis H37Rv 83332 pos
# echo for inj661 reverse
# python mainclean_interation_v0.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000962.3.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000962.3_maxsep.csv --file_type 5 --reward 0.1 --iter 10 --cpu 8 --gram positive --name iNJ661_R
# echo for iAF987 reverse
# python mainclean_interation_v0.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/CP000148.1.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/CP000148.1_maxsep.csv --file_type 5 --reward 0.1 --iter 10 --cpu 8 --gram negative --name iAF987_R
## allec reward =0.1
# genome ORGID ORGNASIM
# t1 iLJ478 NC_000853.1 243274 Thermotoga maritima MSB8 neg
# t2 iJN1463 NC_002947.4 160488 Pseudomonas putida KT2440 neg
# t2 iCN900 AM180355.1 272563 Clostridioides difficile 630 pos
# t4 iAF1260 NC_000913.3 83333 Escherichia coli str. K-12 substr. MG1655 neg
# t4 iAF987 CP000148.1 269799 Geobacter metallireducens GS-15 neg
# t5 iNJ661 NC_000962.3 83332 Mycobacterium tuberculosis H37Rv pos
# t4 iYO844 AL009126.3 224308 Bacillus subtilis subsp. subtilis str. 168 pos
python mainclean_interation_v2.py \
--input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta \
--cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl \
--file_type 7 --reward 0.1 --iter 10 --cpu 8 --gram negative --block_flage 0 --flux_flage 0 --name iLJ478_allec
python mainclean_interation_v2.py \
--input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_002947.4_t2.fasta \
--cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_002947.4_t2_maxsep_df.pkl \
--file_type 7 --reward 0.1 --iter 10 --cpu 8 --gram negative --block_flage 0 --flux_flage 0 --name iJN1463_allec
# python mainclean_interation_v2.py \
# --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta \
# --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl \
# --file_type 7 --reward 0.1 --iter 10 --cpu 8 --gram positive --block_flage 0 --flux_flage 0 --name iCN900_allec
# python mainclean_interation_v2.py \
# --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000913.3_t4.fasta \
# --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000913.3_t4_maxsep_df.pkl \
# --file_type 7 --reward 0.1 --iter 10 --cpu 8 --gram negative --block_flage 0 --flux_flage 0 --name iAF1260_allec
# python mainclean_interation_v2.py \
# --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/CP000148.1_t4.fasta \
# --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/CP000148.1_t4_maxsep_df.pkl \
# --file_type 7 --reward 0.1 --iter 10 --cpu 8 --gram negative --block_flage 0 --flux_flage 0 --name iAF987_allec
python mainclean_interation_v2.py \
--input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000962.3_t5.fasta \
--cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000962.3_t5_maxsep_df.pkl \
--file_type 7 --reward 0.1 --iter 10 --cpu 8 --gram positive --block_flage 0 --flux_flage 0 --name iNJ661_allec
python mainclean_interation_v2.py \
--input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/AL009126.3_t4.fasta \
--cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/AL009126.3_t4_maxsep_df.pkl \
--file_type 7 --reward 0.1 --iter 10 --cpu 8 --gram positive --block_flage 0 --flux_flage 0 --name iYO844_allec
# AL009126.3_t4_maxsep_df.pkl
# AM180355.1_t2_maxsep_df.pkl
# CP000148.1_t4_maxsep_df.pkl
# NC_000853.1_t1_maxsep_df.pkl
# NC_000913.3_t4_maxsep_df.pkl
# NC_000962.3_t5_maxsep_df.pkl
# NC_002947.4_t2_maxsep_df.pkl
# AL009126.3_t4.fasta
# AM180355.1_t2.fasta
# CP000148.1_t4.fasta
# NC_000853.1_t1.fasta
# NC_000913.3_t4.fasta
# NC_000962.3_t5.fasta
# NC_002947.4_t2.fasta