The data is from this link. Here we use: d27, d41_1, and d41_2

1 Output directory

$ cd /project2/xinhe/yanyul/deep_variant/yanyu/deep_brain
$ mkdir test/0628_binize_ATACseq/

2 Region to bin (bin size = 200 bp)

$ python my_scripts/0_region2bins.py data/GSM1820082_d27_fdr0.05.hot.bed.sorted.intersect test/1012_gse70823_binize/
bedtools merge -i test/1012_gse70823_binize//GSM1820082_d27_fdr0.05.hot.bed.sorted_bin200.bed.sorted -d -1 -c 4,5 -o collapse,collapse > test/1012_gse70823_binize//GSM1820082_d27_fdr0.05.hot.bed.sorted_bin200.bed.sorted.merged
$ python my_scripts/0_region2bins.py data/GSM1820085_d411_fdr0.05.hot.bed.sorted.intersect test/1012_gse70823_binize/
bedtools merge -i test/1012_gse70823_binize//GSM1820085_d411_fdr0.05.hot.bed.sorted_bin200.bed.sorted -d -1 -c 4,5 -o collapse,collapse > test/1012_gse70823_binize//GSM1820085_d411_fdr0.05.hot.bed.sorted_bin200.bed.sorted.merged
$ python my_scripts/0_region2bins.py data/GSM1820087_d412_fdr0.05.hot.bed.sorted.intersect test/1012_gse70823_binize/
bedtools merge -i test/1012_gse70823_binize//GSM1820087_d412_fdr0.05.hot.bed.sorted_bin200.bed.sorted -d -1 -c 4,5 -o collapse,collapse > test/1012_gse70823_binize//GSM1820087_d412_fdr0.05.hot.bed.sorted_bin200.bed.sorted.merged

3 Label bins

3.1 Prepare input for wrapper_label_intervals.py

$ ls data/GSM1820082_d27_fdr0.05.hot.bed > test/1012_gse70823_binize/d27.txt
$ ls data/GSM1820085_d411_fdr0.05.hot.bed > test/1012_gse70823_binize/d41_1.txt
$ ls data/GSM1820087_d412_fdr0.05.hot.bed > test/1012_gse70823_binize/d41_2.txt 
$ cat test/1012_gse70823_binize/*txt
data/GSM1820082_d27_fdr0.05.hot.bed
data/GSM1820085_d411_fdr0.05.hot.bed
data/GSM1820087_d412_fdr0.05.hot.bed

3.2 Run wrapper_label_intervals.py

$ python my_scripts/wrapper_label_intervals.py test/1012_gse70823_binize/GSM1820082_d27_fdr0.05.hot.bed.sorted_bin200.bed.sorted.merged.final test/1012_gse70823_binize/d27.txt test/1012_gse70823_binize/
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
mkdir test/1012_gse70823_binize//d27.txt_out
>>> working on data/GSM1820082_d27_fdr0.05.hot.bed
>>> >>> sort data/GSM1820082_d27_fdr0.05.hot.bed
>>> >>> checking data/GSM1820082_d27_fdr0.05.hot.bed
>>> >>> number of columns data/GSM1820082_d27_fdr0.05.hot.bed
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
>>> >>> intersecting data/GSM1820082_d27_fdr0.05.hot.bed
>>> previous = 119778, after = 119778
$ python my_scripts/wrapper_label_intervals.py test/1012_gse70823_binize/GSM1820085_d411_fdr0.05.hot.bed.sorted_bin200.bed.sorted.merged.final test/1012_gse70823_binize/d41_1.txt test/1012_gse70823_binize/
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
mkdir test/1012_gse70823_binize//d41_1.txt_out
>>> working on data/GSM1820085_d411_fdr0.05.hot.bed
>>> >>> sort data/GSM1820085_d411_fdr0.05.hot.bed
>>> >>> checking data/GSM1820085_d411_fdr0.05.hot.bed
>>> >>> number of columns data/GSM1820085_d411_fdr0.05.hot.bed
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
>>> >>> intersecting data/GSM1820085_d411_fdr0.05.hot.bed
>>> previous = 45253, after = 45253
$ python my_scripts/wrapper_label_intervals.py test/1012_gse70823_binize/GSM1820087_d412_fdr0.05.hot.bed.sorted_bin200.bed.sorted.merged.final test/1012_gse70823_binize/d41_2.txt test/1012_gse70823_binize/
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
mkdir test/1012_gse70823_binize//d41_2.txt_out
>>> working on data/GSM1820087_d412_fdr0.05.hot.bed
>>> >>> sort data/GSM1820087_d412_fdr0.05.hot.bed
>>> >>> checking data/GSM1820087_d412_fdr0.05.hot.bed
>>> >>> number of columns data/GSM1820087_d412_fdr0.05.hot.bed
awk: cmd. line:1: (FILENAME=- FNR=4097) fatal: print to "standard output" failed (Broken pipe)
cat: write error: Broken pipe
>>> >>> intersecting data/GSM1820087_d412_fdr0.05.hot.bed
>>> previous = 77612, after = 77612

4 Bin to input format

4.1 Bin to fasta

$ python my_scripts/2_bin2seq.py test/1012_gse70823_binize/GSM1820082_d27_fdr0.05.hot.bed.sorted_bin200.bed.sorted.merged.final 
$ python my_scripts/2_bin2seq.py test/1012_gse70823_binize/GSM1820085_d411_fdr0.05.hot.bed.sorted_bin200.bed.sorted.merged.final 
$ python my_scripts/2_bin2seq.py test/1012_gse70823_binize/GSM1820087_d412_fdr0.05.hot.bed.sorted_bin200.bed.sorted.merged.final

4.2 Line number of illegal bin

No illegal bin is generated.

5 Fasta to hdf5

$ python ../preprocessing/my_scripts/2_seq2input.py test/1012_gse70823_binize/GSM1820082_d27_fdr0.05.hot.bed.sorted_bin200.bed.sorted.merged.final.expended.fa test/1012_gse70823_binize/d27.txt_out/
$ python ../preprocessing/my_scripts/2_seq2input.py test/1012_gse70823_binize/GSM1820085_d411_fdr0.05.hot.bed.sorted_bin200.bed.sorted.merged.final.expended.fa test/1012_gse70823_binize/d41_1.txt_out/
$ python ../preprocessing/my_scripts/2_seq2input.py test/1012_gse70823_binize/GSM1820087_d412_fdr0.05.hot.bed.sorted_bin200.bed.sorted.merged.final.expended.fa test/1012_gse70823_binize/d41_2.txt_out/