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run.fullanalysis.bh
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run.fullanalysis.bh
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##!/usr/bash
## First time bootstrap with C and loose cutoff
./metalCoordinations.pl ../metalPDB/protein_list_Zn.txt Zn -bs ../output_zn/stats -bondLength ../output_zn/bondlength.withC.txt &
./metalCoordinations.pl ../metalPDB/protein_list_Ca.txt Ca -bs ../output_ca/stats -bondLength ../output_ca/bondlength.withC.txt &
./metalCoordinations.pl ../metalPDB/protein_list_Fe.txt Fe -bs ../output_fe/stats -bondLength ../output_fe/bondlength.withC.txt &
./metalCoordinations.pl ../metalPDB/protein_list_Na.txt Na -bs ../output_na/stats -bondLength ../output_na/bondlength.withC.txt &
./metalCoordinations.pl ../metalPDB/protein_list_Mg.txt Mg -bs ../output_mg/stats -bondLength ../output_mg/bondlength.withC.txt &
## Calculate cutoff and elements for each metal
## bondlength.histogram.manuscript.R
## Second bootstrap with updated cutoff and without C and low abundant elements, and get bootstrap bondlength for blstd-resolution slope
nice -10 ./metalCoordinations.pl ../metalPDB/protein_list_Zn.txt Zn 2.782 SON -bs ../output_zn/stats.bs -bondLength ../output_zn/bondlength.noC.txt &
nice -10 ./metalCoordinations.pl ../metalPDB/protein_list_Mg.txt Mg 2.892 ON -bs ../output_mg/stats.bs -bondLength ../output_mg/bondlength.noC.txt &
nice -10 ./metalCoordinations.pl ../metalPDB/protein_list_Ca.txt Ca 3.092 O -bs ../output_ca/stats.bs -bondLength ../output_ca/bondlength.noC.txt &
nice -10 ./metalCoordinations.pl ../metalPDB/protein_list_Fe.txt Fe 2.639 SON -bs ../output_fe/stats.bs -bondLength ../output_fe/bondlength.noC.txt &
nice -10 ./metalCoordinations.pl ../metalPDB/protein_list_Na.txt Na 3.317 ON -bs ../output_na/stats.bs -bondLength ../output_na/bondlength.noC.txt &
## Calculate the overall slope
## blVsRes.overlaidall.R
## Update the blstd-resolution slope in the perl code, and get all options output
./metalCoordinations.pl ../metalPDB/protein_list_Zn.txt Zn 2.782 SON -dd ../output_zn/stats.r -r ../output_zn/r.allLig.txt -rf ../output_zn/rf.smallest.txt -s a s ../output_zn/seqs.ATOM.shell.txt -s s s ../output_zn/seqs.SEQRES.shell.txt -s s b ../output_zn/seqs.SEQRES.bind.txt -bondLength ../output_zn/bondlength.r.txt &
./metalCoordinations.pl ../metalPDB/protein_list_Mg.txt Mg 2.892 ON -dd ../output_mg/stats.r -r ../output_mg/r.allLig.txt -rf ../output_mg/rf.smallest.txt -s a s ../output_mg/seqs.ATOM.shell.txt -s s s ../output_mg/seqs.SEQRES.shell.txt -s s b ../output_mg/seqs.SEQRES.bind.txt -bondLength ../output_mg/bondlength.r.txt &
./metalCoordinations.pl ../metalPDB/protein_list_Ca.txt Ca 3.092 O -dd ../output_ca/stats.r -r ../output_ca/r.allLig.txt -rf ../output_ca/rf.smallest.txt -s a s ../output_ca/seqs.ATOM.shell.txt -s s s ../output_ca/seqs.SEQRES.shell.txt -s s b ../output_ca/seqs.SEQRES.bind.txt -bondLength ../output_ca/bondlength.r.txt &
./metalCoordinations.pl ../metalPDB/protein_list_Fe.txt Fe 2.639 SON -dd ../output_fe/stats.r -r ../output_fe/r.allLig.txt -rf ../output_fe/rf.smallest.txt -s a s ../output_fe/seqs.ATOM.shell.txt -s s s ../output_fe/seqs.SEQRES.shell.txt -s s b ../output_fe/seqs.SEQRES.bind.txt -bondLength ../output_fe/bondlength.r.txt &
./metalCoordinations.pl ../metalPDB/protein_list_Na.txt Na 3.317 O -dd ../output_na/stats.r -r ../output_na/r.allLig.txt -rf ../output_na/rf.smallest.txt -s a s ../output_na/seqs.ATOM.shell.txt -s s s ../output_na/seqs.SEQRES.shell.txt -s s b ../output_na/seqs.SEQRES.bind.txt -bondLength ../output_na/bondlength.r.txt &
## sequence alignment
./seq_alignment.R ../output_zn/
./seq_alignment.R ../output_mg/
./seq_alignment.R ../output_ca/
./seq_alignment.R ../output_fe/
./seq_alignment.R ../output_na/
## non redundant test
./nonRedundancy.R ../output_zn/
./nonRedundancy.R ../output_mg/
./nonRedundancy.R ../output_ca/
./nonRedundancy.R ../output_fe/
./nonRedundancy.R ../output_na/
## write fasta file
./write_fasta.R ../output_zn/ && ./write_fasta.R ../output_mg/ && ./write_fasta.R ../output_ca/ && ./write_fasta.R ../output_fe/ && ./write_fasta.R ../output_na/
## interproscan
output_dir=/mlab/data/sen/projects/metal/go_ec_analysis/output_zn
/mlab/data/software/interproscan-5.18-57.0/interproscan.sh -i $output_dir/non_redundant.fa -f tsv -iprlookup -pa -goterms -o $output_dir/non_redundant.ipr.tsv
output_dir=/mlab/data/sen/projects/metal/go_ec_analysis/output_mg
/mlab/data/software/interproscan-5.18-57.0/interproscan.sh -i $output_dir/non_redundant.fa -f tsv -iprlookup -pa -goterms -o $output_dir/non_redundant.ipr.tsv
output_dir=/mlab/data/sen/projects/metal/go_ec_analysis/output_ca
/mlab/data/software/interproscan-5.18-57.0/interproscan.sh -i $output_dir/non_redundant.fa -f tsv -iprlookup -pa -goterms -o $output_dir/non_redundant.ipr.tsv
output_dir=/mlab/data/sen/projects/metal/go_ec_analysis/output_fe
/mlab/data/software/interproscan-5.18-57.0/interproscan.sh -i $output_dir/non_redundant.fa -f tsv -iprlookup -pa -goterms -o $output_dir/non_redundant.ipr.tsv
output_dir=/mlab/data/sen/projects/metal/go_ec_analysis/output_na
/mlab/data/software/interproscan-5.18-57.0/interproscan.sh -i $output_dir/non_redundant.fa -f tsv -iprlookup -pa -goterms -o $output_dir/non_redundant.ipr.tsv
## random forest
./rf.smallAngle.R ../output_zn 60 70
./rf.smallAngle.R ../output_mg 58 68
./rf.smallAngle.R ../output_ca 55 65
./rf.smallAngle.R ../output_fe 63 73
./rf.smallAngle.R ../output_na 50 65
# Zn
## make folder for each condition
mkdir ../output_zn/root_afterRF
cp ../output_zn/* ../output_zn/root_afterRF/
cp -r ../output_zn/root_afterRF ../output_zn/allLig
cp -r ../output_zn/root_afterRF ../output_zn/4ligand
cp -r ../output_zn/root_afterRF ../output_zn/5ligand
cp -r ../output_zn/root_afterRF ../output_zn/6ligand
## kmeans
nice -10 ./kmeans.mnr.optimalk.R ../output_zn/allLig all 6
nice -10 ./kmeans.mnr.optimalk.R ../output_zn/4ligand 4 6
nice -10 ./kmeans.mnr.optimalk.R ../output_zn/5ligand 5 6
nice -10 ./kmeans.mnr.optimalk.R ../output_zn/6ligand 6 6
nice -10 ./functional_characterization.R ../output_zn/allLig && nice -10 ./measures.vs.k.R ../output_zn/allLig 6 && ./cluster_metric_graphs.R ../output_zn/allLig
nice -10 ./functional_characterization.R ../output_zn/4ligand && nice -10 ./measures.vs.k.R ../output_zn/4ligand 6 && ./cluster_metric_graphs.R ../output_zn/4ligand
nice -10 ./functional_characterization.R ../output_zn/5ligand && nice -10 ./measures.vs.k.R ../output_zn/5ligand 6 && ./cluster_metric_graphs.R ../output_zn/5ligand
nice -10 ./functional_characterization.R ../output_zn/6ligand && nice -10 ./measures.vs.k.R ../output_zn/6ligand 6 && ./cluster_metric_graphs.R ../output_zn/6ligand
## Mg
mkdir ../output_mg/root_afterRF
cp ../output_mg/* ../output_mg/root_afterRF/
cp -r ../output_mg/root_afterRF ../output_mg/allLig
cp -r ../output_mg/root_afterRF ../output_mg/4ligand
cp -r ../output_mg/root_afterRF ../output_mg/5ligand
cp -r ../output_mg/root_afterRF ../output_mg/6ligand
nice -10 ./kmeans.mnr.optimalk.R ../output_mg/allLig all 6
nice -10 ./kmeans.mnr.optimalk.R ../output_mg/4ligand 4 6
nice -10 ./kmeans.mnr.optimalk.R ../output_mg/5ligand 5 6
nice -10 ./kmeans.mnr.optimalk.R ../output_mg/6ligand 6 6
nice -10 ./functional_characterization.R ../output_mg/allLig && nice -10 ./measures.vs.k.R ../output_mg/allLig 6 && ./cluster_metric_graphs.R ../output_mg/allLig
nice -10 ./functional_characterization.R ../output_mg/4ligand && nice -10 ./measures.vs.k.R ../output_mg/4ligand 6 && ./cluster_metric_graphs.R ../output_mg/4ligand
nice -10 ./functional_characterization.R ../output_mg/5ligand && nice -10 ./measures.vs.k.R ../output_mg/5ligand 6 && ./cluster_metric_graphs.R ../output_mg/5ligand
nice -10 ./functional_characterization.R ../output_mg/6ligand && nice -10 ./measures.vs.k.R ../output_mg/6ligand 6 && ./cluster_metric_graphs.R ../output_mg/6ligand
## Ca
mkdir ../output_ca/root_afterRF
cp ../output_ca/* ../output_ca/root_afterRF/
cp -r ../output_ca/root_afterRF ../output_ca/allLig
cp -r ../output_ca/root_afterRF ../output_ca/4ligand
cp -r ../output_ca/root_afterRF ../output_ca/5ligand
cp -r ../output_ca/root_afterRF ../output_ca/6ligand
cp -r ../output_ca/root_afterRF ../output_ca/7ligand
cp -r ../output_ca/root_afterRF ../output_ca/8ligand
nice -10 ./kmeans.mnr.optimalk.R ../output_ca/allLig all 6
nice -10 ./kmeans.mnr.optimalk.R ../output_ca/4ligand 4 6
nice -10 ./kmeans.mnr.optimalk.R ../output_ca/5ligand 5 6
nice -10 ./kmeans.mnr.optimalk.R ../output_ca/6ligand 6 6
nice -10 ./kmeans.mnr.optimalk.R ../output_ca/7ligand 7 6
nice -10 ./kmeans.mnr.optimalk.R ../output_ca/8ligand 8 6
nice -10 ./functional_characterization.R ../output_ca/allLig && nice -10 ./measures.vs.k.R ../output_ca/allLig 6 && ./cluster_metric_graphs.R ../output_ca/allLig
nice -10 ./functional_characterization.R ../output_ca/4ligand && nice -10 ./measures.vs.k.R ../output_ca/4ligand 6 && ./cluster_metric_graphs.R ../output_ca/4ligand
nice -10 ./functional_characterization.R ../output_ca/5ligand && nice -10 ./measures.vs.k.R ../output_ca/5ligand 6 && ./cluster_metric_graphs.R ../output_ca/5ligand
nice -10 ./functional_characterization.R ../output_ca/6ligand && nice -10 ./measures.vs.k.R ../output_ca/6ligand 6 && ./cluster_metric_graphs.R ../output_ca/6ligand
nice -10 ./functional_characterization.R ../output_ca/7ligand && nice -10 ./measures.vs.k.R ../output_ca/7ligand 6 && ./cluster_metric_graphs.R ../output_ca/7ligand
nice -10 ./functional_characterization.R ../output_ca/8ligand && nice -10 ./measures.vs.k.R ../output_ca/8ligand 6 && ./cluster_metric_graphs.R ../output_ca/8ligand
## Fe
mkdir ../output_fe/root_afterRF
cp ../output_fe/* ../output_fe/root_afterRF/
cp -r ../output_fe/root_afterRF ../output_fe/allLig
cp -r ../output_fe/root_afterRF ../output_fe/4ligand
cp -r ../output_fe/root_afterRF ../output_fe/5ligand
cp -r ../output_fe/root_afterRF ../output_fe/6ligand
cp -r ../output_fe/root_afterRF ../output_fe/noheme
nice -10 ./kmeans.mnr.optimalk.R ../output_fe/allLig all 6
nice -10 ./kmeans.mnr.optimalk.R ../output_fe/4ligand 4 6
nice -10 ./kmeans.mnr.optimalk.R ../output_fe/5ligand 5 6
nice -10 ./kmeans.mnr.optimalk.R ../output_fe/6ligand 6 6
nice -10 ./kmeans.mnr.optimalk.R ../output_fe/noheme noheme 6
nice -10 ./functional_characterization.R ../output_fe/allLig && nice -10 ./measures.vs.k.R ../output_fe/allLig 6 && ./cluster_metric_graphs.R ../output_fe/allLig
nice -10 ./functional_characterization.R ../output_fe/4ligand && nice -10 ./measures.vs.k.R ../output_fe/4ligand 6 && ./cluster_metric_graphs.R ../output_fe/4ligand
nice -10 ./functional_characterization.R ../output_fe/5ligand && nice -10 ./measures.vs.k.R ../output_fe/5ligand 6 && ./cluster_metric_graphs.R ../output_fe/5ligand
nice -10 ./functional_characterization.R ../output_fe/6ligand && nice -10 ./measures.vs.k.R ../output_fe/6ligand 6 && ./cluster_metric_graphs.R ../output_fe/6ligand
nice -10 ./functional_characterization.R ../output_fe/noheme && nice -10 ./measures.vs.k.R ../output_fe/noheme 6 && ./cluster_metric_graphs.R ../output_fe/noheme
## Na
mkdir ../output_na/root_afterRF
cp ../output_na/* ../output_na/root_afterRF/
cp -r ../output_na/root_afterRF ../output_na/allLig
cp -r ../output_na/root_afterRF ../output_na/4ligand
cp -r ../output_na/root_afterRF ../output_na/5ligand
cp -r ../output_na/root_afterRF ../output_na/6ligand
nice -10 ./kmeans.mnr.optimalk.R ../output_na/allLig all 6
nice -10 ./kmeans.mnr.optimalk.R ../output_na/4ligand 4 6
nice -10 ./kmeans.mnr.optimalk.R ../output_na/5ligand 5 6
nice -10 ./kmeans.mnr.optimalk.R ../output_na/6ligand 6 6
nice -10 ./functional_characterization.R ../output_na/allLig && nice -10 ./measures.vs.k.R ../output_na/allLig 6 && ./cluster_metric_graphs.R ../output_na/allLig
nice -10 ./functional_characterization.R ../output_na/4ligand && nice -10 ./measures.vs.k.R ../output_na/4ligand 6 && ./cluster_metric_graphs.R ../output_na/4ligand
nice -10 ./functional_characterization.R ../output_na/5ligand && nice -10 ./measures.vs.k.R ../output_na/5ligand 6 && ./cluster_metric_graphs.R ../output_na/5ligand
nice -10 ./functional_characterization.R ../output_na/6ligand && nice -10 ./measures.vs.k.R ../output_na/6ligand 6 && ./cluster_metric_graphs.R ../output_na/6ligand
nice -10 ./functional_characterization.R ../output_na/7ligand && nice -10 ./measures.vs.k.R ../output_na/7ligand 6 && ./cluster_metric_graphs.R ../output_na/7ligand
## Combined
cat ../output_zn/r.allLig.txt ../output_mg/r.allLig.txt ../output_ca/r.allLig.txt ../output_fe/r.allLig.txt ../output_na/r.allLig.txt > ../output_all/r.allLig.txt
cat ../output_zn/rf.smallest.txt ../output_mg/rf.smallest.txt ../output_ca/rf.smallest.txt ../output_fe/rf.smallest.txt ../output_na/rf.smallest.txt > ../output_all/rf.smallest.txt
cat ../output_zn/seqs.SEQRES.shell.txt ../output_mg/seqs.SEQRES.shell.txt ../output_ca/seqs.SEQRES.shell.txt ../output_fe/seqs.SEQRES.shell.txt ../output_na/seqs.SEQRES.shell.txt > ../output_all/seqs.SEQRES.shell.txt
cat ../output_zn/seqs.SEQRES.bind.txt ../output_mg/seqs.SEQRES.bind.txt ../output_ca/seqs.SEQRES.bind.txt ../output_fe/seqs.SEQRES.bind.txt ../output_na/seqs.SEQRES.bind.txt > ../output_all/seqs.SEQRES.bind.txt
cat ../output_zn/seqs.ATOM.shell.txt ../output_mg/seqs.ATOM.shell.txt ../output_ca/seqs.ATOM.shell.txt ../output_fe/seqs.ATOM.shell.txt ../output_na/seqs.ATOM.shell.txt > ../output_all/seqs.ATOM.shell.txt
cat ../output_zn/ia.cutoff/probs.txt ../output_mg/ia.cutoff/probs.txt ../output_ca/ia.cutoff/probs.txt ../output_fe/ia.cutoff/probs.txt ../output_na/ia.cutoff/probs.txt > ../output_all/ia.cutoff/probs.txt
cat ../output_zn/ia.cutoff/probs.leaveOut.txt ../output_mg/ia.cutoff/probs.leaveOut.txt ../output_ca/ia.cutoff/probs.leaveOut.txt ../output_fe/ia.cutoff/probs.leaveOut.txt ../output_na/ia.cutoff/probs.leaveOut.txt > ../output_all/ia.cutoff/probs.leaveOut.txt
cat ../output_zn/non_redundant.ipr.tsv ../output_mg/non_redundant.ipr.tsv ../output_ca/non_redundant.ipr.tsv ../output_fe/non_redundant.ipr.tsv ../output_na/non_redundant.ipr.tsv > ../output_all/non_redundant.ipr.tsv
./combine.nonredundant.R
#./seq_alignment.R ../output_all/
#./nonRedundancy.R ../output_all/
#./write_fasta.R ../output_all/
#output_dir=/mlab/data/sen/projects/metal/go_ec_analysis/output_all
#/mlab/data/software/interproscan-5.18-57.0/interproscan.sh -i $output_dir/non_redundant.fa -f tsv -iprlookup -pa -goterms -o $output_dir/non_redundant.ipr.tsv
## Combined RF prediction results
./combine.predictions.R
mkdir ../output_all/root_afterRF/
cp ../output_all/* ../output_all/root_afterRF/
cp -r ../output_all/root_afterRF ../output_all/allLig
cp -r ../output_all/root_afterRF ../output_all/4ligand
cp -r ../output_all/root_afterRF ../output_all/5ligand
cp -r ../output_all/root_afterRF ../output_all/6ligand
nice -10 ./kmeans.mnr.optimalk.R ../output_all/4ligand 4 6
nice -10 ./kmeans.mnr.optimalk.R ../output_all/5ligand 5 6
nice -10 ./kmeans.mnr.optimalk.R ../output_all/6ligand 6 6
nice -10 ./kmeans.mnr.optimalk.R ../output_all/allLig all 6
nice -10 ./functional_characterization.R ../output_all/4ligand
nice -10 ./functional_characterization.R ../output_all/5ligand
nice -10 ./functional_characterization.R ../output_all/6ligand
nice -10 ./functional_characterization.R ../output_all/allLig
nice -10 ./measures.vs.k.R ../output_all/4ligand 6 && ./cluster_metric_graphs.R ../output_all/4ligand
nice -10 ./measures.vs.k.R ../output_all/5ligand 6 && ./cluster_metric_graphs.R ../output_all/5ligand
nice -10 ./measures.vs.k.R ../output_all/6ligand 6 && ./cluster_metric_graphs.R ../output_all/6ligand
nice -10 ./measures.vs.k.R ../output_all/allLig 6 && ./cluster_metric_graphs.R ../output_all/allLig
#####################
## Tables and Figures
#####################
./getrhop.R zn 4 normal 10 4
./getrhop.R zn 4 combined 11 4
./getrhop.R zn 5 normal 8 2
./getrhop.R zn 5 compressed 7 2
./getrhop.R zn 5 combined 7 2
./getrhop.R zn 6 normal 6 2
./getrhop.R zn 6 combined 7 3
./getrhop.R zn combined normal 7 2
./getrhop.R zn combined compressed 10 3
./getrhop.R zn combined combined 9 1
./getrhop.R mg 4 normal 7 1
./getrhop.R mg 4 combined 13 3
./getrhop.R mg 5 normal 5 1
./getrhop.R mg 5 combined 21 3
./getrhop.R mg 6 normal 5 1
./getrhop.R mg 6 compressed 8 1
./getrhop.R mg 6 combined 6 1
./getrhop.R mg combined normal 11 1
./getrhop.R mg combined compressed 6 2
./getrhop.R mg combined combined 7 3
./getrhop.R ca 4 normal 5 4
./getrhop.R ca 4 combined 5 1
./getrhop.R ca 5 normal 7 3
./getrhop.R ca 5 compressed 6 4
./getrhop.R ca 5 combined 5 1
./getrhop.R ca 6 normal 6 3
./getrhop.R ca 6 compressed 8 2
./getrhop.R ca 6 combined 8 1
./getrhop.R ca 7 normal 8 34
./getrhop.R ca 7 compressed 10 1
./getrhop.R ca 7 combined 11 1
./getrhop.R ca 8 compressed 4 3
./getrhop.R ca 8 combined 10 4
./getrhop.R ca combined normal 6 2
./getrhop.R ca combined compressed 10 4
./getrhop.R ca combined combined 13 4
./getrhop.R fe 4 normal 5 1
./getrhop.R fe 4 combined 5 1
./getrhop.R fe 5 normal 7 4
./getrhop.R fe 5 compressed 4 3
./getrhop.R fe 5 combined 10 4
./getrhop.R fe 6 normal 7 1
./getrhop.R fe 6 compressed 4 2
./getrhop.R fe 6 combined 7 1
./getrhop.R fe combined normal 7 1
./getrhop.R fe combined compressed 6 1
./getrhop.R fe combined combined 10 1
./getrhop.R fe noheme normal 10 1
./getrhop.R fe noheme compressed 6 2
./getrhop.R fe noheme combined 10 3
./getrhop.R na 4 normal 10 2
./getrhop.R na 4 combined 7 3
./getrhop.R na 5 normal 10 1
./getrhop.R na 5 combined 7 2
./getrhop.R na 6 normal 6 3
./getrhop.R na 6 combined 7 3
./getrhop.R na combined normal 5 4
./getrhop.R na combined compressed 8 2
./getrhop.R na combined combined 8 3
./getrhop.R combined 4 normal 6 3
./getrhop.R combined 4 compressed 5 1
./getrhop.R combined 4 combined 7 4
./getrhop.R combined 5 normal 9 1
./getrhop.R combined 5 compressed 7 4
./getrhop.R combined 5 combined 7 3
./getrhop.R combined 6 normal 6 1
./getrhop.R combined 6 compressed 12 1
./getrhop.R combined 6 combined 9 1
./getrhop.R combined 7 normal 10 3
./getrhop.R combined 7 compressed 12 3
./getrhop.R combined 7 combined 12 1
./getrhop.R combined 8 normal 6 2
./getrhop.R combined 8 compressed 4 3
./getrhop.R combined 8 combined 10 2
./getrhop.R combined combined normal 7 4
./getrhop.R combined combined compressed 7 3
./getrhop.R combined combined combined 8 4
#######
./center.prob.metallist.R ../output_zn/4ligand/ 10 3 11 7
./center.prob.metallist.R ../output_zn/5ligand/ 8 7 7 7
./center.prob.metallist.R ../output_zn/6ligand/ 6 3 7 7
./center.prob.metallist.R ../output_zn/allLig/ 7 10 9 6
./center.prob.metallist.R ../output_mg/4ligand/ 7 3 13 7
./center.prob.metallist.R ../output_mg/5ligand/ 5 3 21 7
./center.prob.metallist.R ../output_mg/6ligand/ 5 8 6 7
./center.prob.metallist.R ../output_mg/allLig/ 11 6 7 6
./center.prob.metallist.R ../output_ca/4ligand/ 5 3 5 7
./center.prob.metallist.R ../output_ca/5ligand/ 7 6 5 7
./center.prob.metallist.R ../output_ca/6ligand/ 6 8 8 7
./center.prob.metallist.R ../output_ca/7ligand/ 8 10 11 7
./center.prob.metallist.R ../output_ca/8ligand/ 3 4 10 7
./center.prob.metallist.R ../output_ca/allLig/ 6 10 13 6
./center.prob.metallist.R ../output_fe/4ligand/ 5 3 5 7
./center.prob.metallist.R ../output_fe/5ligand/ 7 4 10 7
./center.prob.metallist.R ../output_fe/6ligand/ 7 4 7 7
./center.prob.metallist.R ../output_fe/allLig/ 7 6 10 6
./center.prob.metallist.R ../output_fe/noheme/ 10 6 10 6
./center.prob.metallist.R ../output_na/4ligand/ 10 3 7 7
./center.prob.metallist.R ../output_na/5ligand/ 10 3 7 7
./center.prob.metallist.R ../output_na/6ligand/ 6 3 7 7
./center.prob.metallist.R ../output_na/allLig/ 5 8 8 6
./center.prob.metallist.R ../output_all/4ligand/ 6 5 7 7
./center.prob.metallist.R ../output_all/5ligand/ 9 7 7 7
./center.prob.metallist.R ../output_all/6ligand/ 6 12 9 7
./center.prob.metallist.R ../output_all/7ligand/ 10 12 12 7
./center.prob.metallist.R ../output_all/8ligand/ 6 4 10 7
./center.prob.metallist.R ../output_all/allLig/ 7 7 8 6
#########
./hierarchical.clustering.R ../output_zn/4ligand 10 4 0 0
./hierarchical.clustering.R ../output_zn/5ligand 8 2 7 2
./hierarchical.clustering.R ../output_zn/6ligand 6 2 0 0
./hierarchical.clustering.R ../output_zn/allLig 7 2 10 3
./hierarchical.clustering.R ../output_mg/4ligand 7 1 0 0
./hierarchical.clustering.R ../output_mg/5ligand 5 1 0 0
./hierarchical.clustering.R ../output_mg/6ligand 5 1 8 1
./hierarchical.clustering.R ../output_mg/allLig 11 1 6 2
./hierarchical.clustering.R ../output_ca/4ligand 5 4 0 0
./hierarchical.clustering.R ../output_ca/5ligand 7 3 6 4
./hierarchical.clustering.R ../output_ca/6ligand 6 3 8 2
./hierarchical.clustering.R ../output_ca/7ligand 8 3 10 1
./hierarchical.clustering.R ../output_ca/8ligand 0 0 4 3
./hierarchical.clustering.R ../output_ca/allLig 6 2 10 4
./hierarchical.clustering.R ../output_fe/4ligand 5 1 0 0
./hierarchical.clustering.R ../output_fe/5ligand 7 4 4 3
./hierarchical.clustering.R ../output_fe/6ligand 7 1 4 2
./hierarchical.clustering.R ../output_fe/allLig 7 1 6 1
./hierarchical.clustering.R ../output_fe/noheme 10 1 6 2
./hierarchical.clustering.R ../output_na/4ligand 10 2 0 0
./hierarchical.clustering.R ../output_na/5ligand 10 1 0 0
./hierarchical.clustering.R ../output_na/6ligand 6 3 0 0
./hierarchical.clustering.R ../output_na/allLig 5 4 8 2
./hierarchical.clustering.R ../output_all/4ligand 6 3 5 1
./hierarchical.clustering.R ../output_all/5ligand 9 1 7 4
./hierarchical.clustering.R ../output_all/6ligand 6 1 12 1
./hierarchical.clustering.R ../output_all/7ligand 10 3 12 3
./hierarchical.clustering.R ../output_all/8ligand 6 2 4 3
./hierarchical.clustering.R ../output_all/allLig 7 4 7 3