Output directory
$ cd /project2/xinhe/yanyul/deep_variant/yanyu/deep_brain
$ mkdir test/0628_binize_ATACseq/
Region to bin (bin size = 200 bp)
$ python my_scripts/0_region2bins.py data/Noonan_hNSC_50_peaks.bed.sorted.intersect test/0628_binize_ATACseq/
bedtools merge -i test/0628_binize_ATACseq//Noonan_hNSC_50_peaks.bed.sorted_bin200.bed.sorted -d -1 -c 4,5 -o collapse,collapse > test/0628_binize_ATACseq//Noonan_hNSC_50_peaks.bed.sorted_bin200.bed.sorted.merged
$ python my_scripts/0_region2bins.py data/Noonan_hNSC_P15-1_peaks.bed.sorted.intersect test/0628_binize_ATACseq/
bedtools merge -i test/0628_binize_ATACseq//Noonan_hNSC_P15-1_peaks.bed.sorted_bin200.bed.sorted -d -1 -c 4,5 -o collapse,collapse > test/0628_binize_ATACseq//Noonan_hNSC_P15-1_peaks.bed.sorted_bin200.bed.sorted.merged
$ python my_scripts/0_region2bins.py data/Noonan_hNSC_P5-1_peaks.bed.sorted.intersect test/0628_binize_ATACseq/
bedtools merge -i test/0628_binize_ATACseq//Noonan_hNSC_P5-1_peaks.bed.sorted_bin200.bed.sorted -d -1 -c 4,5 -o collapse,collapse > test/0628_binize_ATACseq//Noonan_hNSC_P5-1_peaks.bed.sorted_bin200.bed.sorted.merged
$ python my_scripts/0_region2bins.py data/Noonan_hNSC_P5-2_peaks.bed.sorted.intersect test/0628_binize_ATACseq/
bedtools merge -i test/0628_binize_ATACseq//Noonan_hNSC_P5-2_peaks.bed.sorted_bin200.bed.sorted -d -1 -c 4,5 -o collapse,collapse > test/0628_binize_ATACseq//Noonan_hNSC_P5-2_peaks.bed.sorted_bin200.bed.sorted.merged
Label bins
Run wrapper_label_intervals.py
$ python my_scripts/wrapper_label_intervals.py test/0628_binize_ATACseq/Noonan_hNSC_50_peaks.bed.sorted_bin200.bed.sorted.merged.final test/0628_binize_ATACseq/hNSC_50.txt test/0628_binize_ATACseq/
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
mkdir test/0628_binize_ATACseq//hNSC_50.txt_out
>>> working on data/Noonan_hNSC_50_peaks.bed
>>> >>> sort data/Noonan_hNSC_50_peaks.bed
>>> >>> checking data/Noonan_hNSC_50_peaks.bed
>>> >>> number of columns data/Noonan_hNSC_50_peaks.bed
awk: cmd. line:1: (FILENAME=- FNR=2731) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
>>> >>> intersecting data/Noonan_hNSC_50_peaks.bed
>>> previous = 124826, after = 124826
$ python my_scripts/wrapper_label_intervals.py test/0628_binize_ATACseq/Noonan_hNSC_P15-1_peaks.bed.sorted_bin200.bed.sorted.merged.final test/0628_binize_ATACseq/hNSC_P15-1.txt test/0628_binize_ATACseq/
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
mkdir test/0628_binize_ATACseq//hNSC_P15-1.txt_out
>>> working on data/Noonan_hNSC_P15-1_peaks.bed
>>> >>> sort data/Noonan_hNSC_P15-1_peaks.bed
>>> >>> checking data/Noonan_hNSC_P15-1_peaks.bed
>>> >>> number of columns data/Noonan_hNSC_P15-1_peaks.bed
awk: cmd. line:1: (FILENAME=- FNR=2731) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
>>> >>> intersecting data/Noonan_hNSC_P15-1_peaks.bed
>>> previous = 84105, after = 84105
$ python my_scripts/wrapper_label_intervals.py test/0628_binize_ATACseq/Noonan_hNSC_P5-1_peaks.bed.sorted_bin200.bed.sorted.merged.final test/0628_binize_ATACseq/hNSC_P5-1.txt test/0628_binize_ATACseq/
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
mkdir test/0628_binize_ATACseq//hNSC_P5-1.txt_out
>>> working on data/Noonan_hNSC_P5-1_peaks.bed
>>> >>> sort data/Noonan_hNSC_P5-1_peaks.bed
>>> >>> checking data/Noonan_hNSC_P5-1_peaks.bed
>>> >>> number of columns data/Noonan_hNSC_P5-1_peaks.bed
awk: cmd. line:1: (FILENAME=- FNR=2731) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
>>> >>> intersecting data/Noonan_hNSC_P5-1_peaks.bed
>>> previous = 67160, after = 67160
$ python my_scripts/wrapper_label_intervals.py test/0628_binize_ATACseq/Noonan_hNSC_P5-2_peaks.bed.sorted_bin200.bed.sorted.merged.final test/0628_binize_ATACseq/hNSC_P5-2.txt test/0628_binize_ATACseq/
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
mkdir test/0628_binize_ATACseq//hNSC_P5-2.txt_out
>>> working on data/Noonan_hNSC_P5-2_peaks.bed
>>> >>> sort data/Noonan_hNSC_P5-2_peaks.bed
>>> >>> checking data/Noonan_hNSC_P5-2_peaks.bed
>>> >>> number of columns data/Noonan_hNSC_P5-2_peaks.bed
awk: cmd. line:1: (FILENAME=- FNR=2731) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
>>> >>> intersecting data/Noonan_hNSC_P5-2_peaks.bed
>>> previous = 86563, after = 86563
Fasta to hdf5
$ python ../preprocessing/my_scripts/2_seq2input.py test/0628_binize_ATACseq/Noonan_hNSC_50_peaks.bed.sorted_bin200.bed.sorted.merged.final.expended.fa test/0628_binize_ATACseq/hNSC_50.txt_out/
$ python ../preprocessing/my_scripts/2_seq2input.py test/0628_binize_ATACseq/Noonan_hNSC_P15-1_peaks.bed.sorted_bin200.bed.sorted.merged.final.expended.fa test/0628_binize_ATACseq/hNSC_P15-1.txt_out/
$ python ../preprocessing/my_scripts/2_seq2input.py test/0628_binize_ATACseq/Noonan_hNSC_P5-1_peaks.bed.sorted_bin200.bed.sorted.merged.final.expended.fa test/0628_binize_ATACseq/hNSC_P5-1.txt_out/
$ python ../preprocessing/my_scripts/2_seq2input.py test/0628_binize_ATACseq/Noonan_hNSC_P5-2_peaks.bed.sorted_bin200.bed.sorted.merged.final.expended.fa test/0628_binize_ATACseq/hNSC_P5-2.txt_out/