; matrix-from-patterns  -v 1 -sites -seq Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -pl Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -toppat 100 -max_asmb_nb 50 -max_asmb_width 20 -subst 1 -prefix positions_7nt -flanks 2 -collect_method matrix-scan-quick -logo -cluster none -o Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm
; Input files
;	patterns	Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab
;	sequence	Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta
; Output files
;	sig_matrices_split	Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_matrix_list.tab
;	sig_matrices	Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices.tf
;	count_matrices	Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.txt
;	logo_basename	Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo
;	count_matrices_tf	Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf
;	gibbs_matrices	Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_gibbs_matrices.txt
;	sig_sites	Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft
;	err	Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_err.txt
;	output	Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm
;	log	Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_log.txt
;	links	Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_links.txt
;	assembly	Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm.asmb
; Number of patterns	14
; patterns -> assemblies
/data/rsat/perl-scripts/pattern-assembly -v 1 -i Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab -2str -maxfl 1 -subst 1 -max_asmb_width 20 -toppat 100 -max_asmb_size 50 -max_asmb_width 20 -max_asmb_nb 50 -o Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm.asmb


/data/rsat/perl-scripts/pattern-assembly -v 1 -i Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab -2str -maxfl 1 -subst 1 -max_asmb_width 20 -toppat 100 -max_asmb_size 50 -max_asmb_width 20 -max_asmb_nb 50 -o Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm.asmb
; Number of assemblies	9
; Number of assembled patterns	57
; assemblies -> significance matrices
/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -top 50 -prefix positions_7nt -o Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices.tf


/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -top 50 -prefix positions_7nt -o Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices.tf
; Rescaling significance matrices
/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 100 -o Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_rescaled.tf


/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 100 -o Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_rescaled.tf


/data/rsat/perl-scripts/convert-matrix -from tf -i Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_rescaled.tf -to tab -split  -o Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split; rm -f Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.txt

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m1.tab -name positions_7nt_m1 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m1.tab -name positions_7nt_m1 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m2.tab -name positions_7nt_m2 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m2.tab -name positions_7nt_m2 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m3.tab -name positions_7nt_m3 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m3.tab -name positions_7nt_m3 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m4.tab -name positions_7nt_m4 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m4.tab -name positions_7nt_m4 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m5.tab -name positions_7nt_m5 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m5.tab -name positions_7nt_m5 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m6.tab -name positions_7nt_m6 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m6.tab -name positions_7nt_m6 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m7.tab -name positions_7nt_m7 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m7.tab -name positions_7nt_m7 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m8.tab -name positions_7nt_m8 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m8.tab -name positions_7nt_m8 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m9.tab -name positions_7nt_m9 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft


/data/rsat/bin/matrix-scan-quick -v 1 -i Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test.fasta -m Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_matrices_split_positions_7nt_m9.tab -name positions_7nt_m9 -2str -t 5 -return sites -bgfile Myogenin_Rep2_motifs50/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt >> Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft
; sites -> transfac matrices
/data/rsat/perl-scripts/convert-matrix -v 0 -i Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft -from feature -to transfac -prefix positions_7nt -return counts -return sites -o Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf


/data/rsat/perl-scripts/convert-matrix -v 0 -i Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_sig_sites.ft -from feature -to transfac -prefix positions_7nt -return counts -return sites -o Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf
; transfac-formatted -> tab-formatted matrices
/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf -from transfac -to tab -return counts -return sites -o Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.txt


/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf -from transfac -to tab -return counts -return sites -o Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.txt
; sites -> count matrices
/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf -from tf -to tab -return counts -return sites -return logo -logo_format png -logo_file Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo -o Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_links.txt


/data/rsat/perl-scripts/convert-matrix -v 1 -i Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices.tf -from tf -to tab -return counts -return sites -return logo -logo_format png -logo_file Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_logo -o Myogenin_Rep2_motifs50/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50_pssm_count_matrices_links.txt
; Host name	pedagogix
; Job started	2020-04-13.203149
; Job done	2020-04-13.203208
; Seconds	0.18
;	user	0.18
;	system	0.02
;	cuser	18.64
;	csystem	0.97
