The data is obtained from Yifan containing CN, DN, GA, ips, NSC
$ cd /project2/xinhe/yanyul/deep_variant/yanyu/deep_brain
$ mkdir test/atac-seq_053018_binize$ python my_scripts/0_region2bins.py data/CN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted.intersect test/atac-seq_053018_binize/
bedtools merge -i test/atac-seq_053018_binize//CN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted -d -1 -c 4,5 -o collapse,collapse > test/atac-seq_053018_binize//CN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged
$ python my_scripts/0_region2bins.py data/DN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted.intersect test/atac-seq_053018_binize/
bedtools merge -i test/atac-seq_053018_binize//DN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted -d -1 -c 4,5 -o collapse,collapse > test/atac-seq_053018_binize//DN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged
$ python my_scripts/0_region2bins.py data/GA_all_peaks.narrowPeak.cleaned.hg19.merged.sorted.intersect test/atac-seq_053018_binize/
bedtools merge -i test/atac-seq_053018_binize//GA_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted -d -1 -c 4,5 -o collapse,collapse > test/atac-seq_053018_binize//GA_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged
$ python my_scripts/0_region2bins.py data/CN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted.intersect test/atac-seq_053018_binize/
bedtools merge -i test/atac-seq_053018_binize//CN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted -d -1 -c 4,5 -o collapse,collapse > test/atac-seq_053018_binize//CN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged
$ python my_scripts/0_region2bins.py data/NSC_all_peaks.narrowPeak.cleaned.hg19.merged.sorted.intersect test/atac-seq_053018_binize/
bedtools merge -i test/atac-seq_053018_binize//NSC_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted -d -1 -c 4,5 -o collapse,collapse > test/atac-seq_053018_binize//NSC_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.mergedwrapper_label_intervals.py$ ls data/CN_all_peaks.narrowPeak.cleaned.hg19.merged > test/atac-seq_053018_binize/CN.txt
$ ls data/DN_all_peaks.narrowPeak.cleaned.hg19.merged > test/atac-seq_053018_binize/DN.txt
$ ls data/GA_all_peaks.narrowPeak.cleaned.hg19.merged > test/atac-seq_053018_binize/GA.txt
$ ls data/ips_all_peaks.narrowPeak.cleaned.hg19.merged > test/atac-seq_053018_binize/ips.txt
$ ls data/NSC_all_peaks.narrowPeak.cleaned.hg19.merged > test/atac-seq_053018_binize/NSC.txt
$ cat test/atac-seq_053018_binize/*txt
data/CN_all_peaks.narrowPeak.cleaned.hg19.merged
data/DN_all_peaks.narrowPeak.cleaned.hg19.merged
data/GA_all_peaks.narrowPeak.cleaned.hg19.merged
data/ips_all_peaks.narrowPeak.cleaned.hg19.merged
data/NSC_all_peaks.narrowPeak.cleaned.hg19.mergedwrapper_label_intervals.py$ python my_scripts/wrapper_label_intervals.py test/atac-seq_053018_binize/CN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final test/atac-seq_053018_binize/CN.txt test/atac-seq_053018_binize/
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
mkdir test/atac-seq_053018_binize//CN.txt_out
>>> working on data/CN_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> sort data/CN_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> checking data/CN_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> number of columns data/CN_all_peaks.narrowPeak.cleaned.hg19.merged
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
>>> >>> intersecting data/CN_all_peaks.narrowPeak.cleaned.hg19.merged
>>> previous = 249590, after = 249590
$ python my_scripts/wrapper_label_intervals.py test/atac-seq_053018_binize/DN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final test/atac-seq_053018_binize/DN.txt test/atac-seq_053018_binize/
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
mkdir test/atac-seq_053018_binize//DN.txt_out
>>> working on data/DN_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> sort data/DN_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> checking data/DN_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> number of columns data/DN_all_peaks.narrowPeak.cleaned.hg19.merged
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
>>> >>> intersecting data/DN_all_peaks.narrowPeak.cleaned.hg19.merged
>>> previous = 278092, after = 278092
$ python my_scripts/wrapper_label_intervals.py test/atac-seq_053018_binize/GA_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final test/atac-seq_053018_binize/GA.txt test/atac-seq_053018_binize/
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
mkdir test/atac-seq_053018_binize//GA.txt_out
>>> working on data/GA_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> sort data/GA_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> checking data/GA_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> number of columns data/GA_all_peaks.narrowPeak.cleaned.hg19.merged
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
>>> >>> intersecting data/GA_all_peaks.narrowPeak.cleaned.hg19.merged
>>> previous = 329787, after = 329787
$ python my_scripts/wrapper_label_intervals.py test/atac-seq_053018_binize/ips_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final test/atac-seq_053018_binize/ips.txt test/atac-seq_053018_binize/
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
mkdir test/atac-seq_053018_binize//ips.txt_out
>>> working on data/ips_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> sort data/ips_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> checking data/ips_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> number of columns data/ips_all_peaks.narrowPeak.cleaned.hg19.merged
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
>>> >>> intersecting data/ips_all_peaks.narrowPeak.cleaned.hg19.merged
>>> previous = 344669, after = 344669
$ python my_scripts/wrapper_label_intervals.py test/atac-seq_053018_binize/NSC_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final test/atac-seq_053018_binize/NSC.txt test/atac-seq_053018_binize/
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
mkdir test/atac-seq_053018_binize//NSC.txt_out
>>> working on data/NSC_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> sort data/NSC_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> checking data/NSC_all_peaks.narrowPeak.cleaned.hg19.merged
>>> >>> number of columns data/NSC_all_peaks.narrowPeak.cleaned.hg19.merged
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
>>> >>> intersecting data/NSC_all_peaks.narrowPeak.cleaned.hg19.merged
>>> previous = 248686, after = 248686$ python my_scripts/2_bin2seq.py test/atac-seq_053018_binize/CN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final
Feature (chr17:81194400-81195400) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81194600-81195600) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81194800-81195800) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195000-81196000) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195200-81196200) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195400-81196400) beyond the length of chr17 size (81195210 bp). Skipping.
$ python my_scripts/2_bin2seq.py test/atac-seq_053018_binize/DN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final
Feature (chr17:81194400-81195400) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81194600-81195600) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81194800-81195800) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195000-81196000) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195200-81196200) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195400-81196400) beyond the length of chr17 size (81195210 bp). Skipping.
$ python my_scripts/2_bin2seq.py test/atac-seq_053018_binize/GA_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final
Feature (chr17:81194400-81195400) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81194600-81195600) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81194800-81195800) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195000-81196000) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195200-81196200) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195400-81196400) beyond the length of chr17 size (81195210 bp). Skipping.
$ python my_scripts/2_bin2seq.py test/atac-seq_053018_binize/ips_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final
Feature (chr17:81194400-81195400) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81194600-81195600) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81194800-81195800) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195000-81196000) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195200-81196200) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195400-81196400) beyond the length of chr17 size (81195210 bp). Skipping.
$ python my_scripts/2_bin2seq.py test/atac-seq_053018_binize/NSC_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final
Feature (chr17:81194400-81195400) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81194600-81195600) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81194800-81195800) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195000-81196000) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195200-81196200) beyond the length of chr17 size (81195210 bp). Skipping.
Feature (chr17:81195400-81196400) beyond the length of chr17 size (81195210 bp). Skipping.$ cat test/atac-seq_053018_binize/CN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final | grep -n 81194400 -A 7
548979:chr17 81194200 81194400 548979 3,4 left,left
548980:chr17 81194400 81194600 548980 2,3 left,left
548981-chr17 81194600 81194800 548981 1,2 left,left
548982-chr17 81194800 81195000 548982 0,1 hitted,left
548983-chr17 81195000 81195200 548983 1,0 right,hitted
548984-chr17 81195200 81195400 548984 2,1 right,right
548985-chr17 81195400 81195600 548985 2,3 right,right
548986-chr17 81195600 81195800 548986 4,3 right,right
548987-chr17 81195800 81196000 548987 4 right
$ cat test/atac-seq_053018_binize/DN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final | grep -n 81194400 -A 7
726141:chr17 81194200 81194400 726141 4,3 left,left
726142:chr17 81194400 81194600 726142 3,2 left,left
726143-chr17 81194600 81194800 726143 2,1 left,left
726144-chr17 81194800 81195000 726144 1,0 left,hitted
726145-chr17 81195000 81195200 726145 1,0 right,hitted
726146-chr17 81195200 81195400 726146 2,1 right,right
726147-chr17 81195400 81195600 726147 3,2 right,right
726148-chr17 81195600 81195800 726148 4,3 right,right
726149-chr17 81195800 81196000 726149 4 right
$ cat test/atac-seq_053018_binize/GA_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final | grep -n 81194400 -A 7
611601:chr17 81194200 81194400 611601 4,3 left,left
611602:chr17 81194400 81194600 611602 3,2 left,left
611603-chr17 81194600 81194800 611603 2,1 left,left
611604-chr17 81194800 81195000 611604 1,0 left,hitted
611605-chr17 81195000 81195200 611605 1,0 right,hitted
611606-chr17 81195200 81195400 611606 2,1 right,right
611607-chr17 81195400 81195600 611607 3,2 right,right
611608-chr17 81195600 81195800 611608 4,3 right,right
611609-chr17 81195800 81196000 611609 4 right
--
1405927:chr8 81194200 81194400 1405927 4 left
1405928:chr8 81194400 81194600 1405928 3,4 left,left
1405929-chr8 81194600 81194800 1405929 2,3 left,left
1405930-chr8 81194800 81195000 1405930 1,2 left,left
1405931-chr8 81195000 81195200 1405931 0,1 hitted,left
1405932-chr8 81195200 81195400 1405932 1,0 right,hitted
1405933-chr8 81195400 81195600 1405933 2,1 right,right
1405934-chr8 81195600 81195800 1405934 2,3 right,right
1405935-chr8 81195800 81196000 1405935 4,3 right,right
$ cat test/atac-seq_053018_binize/ips_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final | grep -n 81194400 -A 7
273832:chr10 81194200 81194400 273832 4 left
273833:chr10 81194400 81194600 273833 3 left
273834-chr10 81194600 81194800 273834 2 left
273835-chr10 81194800 81195000 273835 1 left
273836-chr10 81195000 81195200 273836 0 hitted
273837-chr10 81195200 81195400 273837 1 right
273838-chr10 81195400 81195600 273838 2 right
273839-chr10 81195600 81195800 273839 3 right
273840-chr10 81195800 81196000 273840 4 right
--
921875:chr17 81194200 81194400 921875 3,4 left,left
921876:chr17 81194400 81194600 921876 2,3 left,left
921877-chr17 81194600 81194800 921877 1,2 left,left
921878-chr17 81194800 81195000 921878 0,1 hitted,left
921879-chr17 81195000 81195200 921879 1,0 right,hitted
921880-chr17 81195200 81195400 921880 2,1 right,right
921881-chr17 81195400 81195600 921881 2,3 right,right
921882-chr17 81195600 81195800 921882 4,3 right,right
921883-chr17 81195800 81196000 921883 4 right
--
2100527:chr8 81194200 81194400 2100527 4 left
2100528:chr8 81194400 81194600 2100528 4,3 left,left
2100529-chr8 81194600 81194800 2100529 3,2 left,left
2100530-chr8 81194800 81195000 2100530 2,1 left,left
2100531-chr8 81195000 81195200 2100531 1,0 left,hitted
2100532-chr8 81195200 81195400 2100532 0,1 hitted,right
2100533-chr8 81195400 81195600 2100533 2,1 right,right
2100534-chr8 81195600 81195800 2100534 3,2 right,right
2100535-chr8 81195800 81196000 2100535 4,3 right,right
$ cat test/atac-seq_053018_binize/NSC_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final | grep -n 81194400 -A 7
533711:chr17 81194200 81194400 533711 3,4 left,left
533712:chr17 81194400 81194600 533712 2,3 left,left
533713-chr17 81194600 81194800 533713 2,1 left,left
533714-chr17 81194800 81195000 533714 0,1 hitted,left
533715-chr17 81195000 81195200 533715 0,1 hitted,right
533716-chr17 81195200 81195400 533716 2,1 right,right
533717-chr17 81195400 81195600 533717 3,2 right,right
533718-chr17 81195600 81195800 533718 4,3 right,right
533719-chr17 81195800 81196000 533719 4 right$ python ../preprocessing/my_scripts/2_seq2input.py test/atac-seq_053018_binize/CN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final.expended.fa test/atac-seq_053018_binize/CN.txt_out/
$ python ../preprocessing/my_scripts/2_seq2input.py test/atac-seq_053018_binize/DN_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final.expended.fa test/atac-seq_053018_binize/DN.txt_out/
$ python ../preprocessing/my_scripts/2_seq2input.py test/atac-seq_053018_binize/GA_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final.expended.fa test/atac-seq_053018_binize/GA.txt_out/
$ python ../preprocessing/my_scripts/2_seq2input.py test/atac-seq_053018_binize/ips_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final.expended.fa test/atac-seq_053018_binize/ips.txt_out/
$ python ../preprocessing/my_scripts/2_seq2input.py test/atac-seq_053018_binize/NSC_all_peaks.narrowPeak.cleaned.hg19.merged.sorted_bin200.bed.sorted.merged.final.expended.fa test/atac-seq_053018_binize/NSC.txt_out/