├── README.md
└── cool2hic.py


/README.md:
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 1 | # Cooler to hic
 2 | 
 3 | Dependences:
 4 | ```
 5 | pip install cooler
 6 | pip install pandas
 7 | ```
 8 | 
 9 | 1, cool2hic.py
10 | 
11 | Transfer cool to matrix.txt.gz.
12 | ```
13 | python3 cool2hic.py -i test.mcool/test.cool -r resolution
14 | ```
15 | 
16 | 
17 | 2, juicer_tools transfer from matrix text to hic.
18 | 
19 | juicer_tools: https://github.com/aidenlab/juicer/wiki/Feature-Annotation
20 | ```
21 | gzip matrix.txt matrix.txt.gz
22 | java -Xmx20g -jar ~/packages/juicer_tools.jar pre -r resolution -d matrix.txt.gz name.hic genome
23 | ```
24 | 


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/cool2hic.py:
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 1 | from optparse import OptionParser
 2 | import cooler
 3 | import pandas as pd
 4 | 
 5 | desc="Transfer cool to hic."
 6 | 
 7 | parser = OptionParser(description=desc)
 8 | 
 9 | parser.add_option("-i", "--input", action="store", type="string",
10 |                   dest="input", help="Input cool or mcool file.", metavar="<file>")
11 | 
12 | parser.add_option("-r", "--resolution", action="store", type="int",
13 |                   dest="res", help="Resolution for the output hic file.", metavar="<int>")
14 | 
15 | (opt, args) = parser.parse_args()
16 | file =  opt.input
17 | resolution = opt.res
18 | 
19 | print("Input file: %s" % file)
20 | print("Resolution: %s" % resolution)
21 | 
22 | #==========================
23 | 
24 | file_type = file.split('.')[len(file.split('.'))-1]
25 | if file_type == 'cool':
26 |     c = cooler.Cooler(file)
27 | if file_type == 'mcool':
28 |     c = cooler.Cooler(file+'::resolutions/'+str(resolution))
29 | 
30 | chrom = c.chroms()[0:len(c.chroms())]
31 | chrom = chrom[~chrom.name.str.contains('_|M')]
32 | chrom = chrom.sort_values('name')
33 | 
34 | for i in chrom.name:
35 |     print(i)
36 |     hic_chr = c.matrix(balance=False, as_pixels=True, join=True).fetch(i)
37 |     hic_chr = hic_chr.iloc[:,[0,1,3,4,6]]
38 |     hic_chr['str1'] = 0
39 |     hic_chr['str2'] = 0
40 |     hic_chr['frag1'] = 0
41 |     hic_chr['frag2'] = 1
42 |     names = ['str1','chrom1','start1','frag1','str2','chrom2','start2','frag2','count']
43 |     hic_chr = hic_chr.reindex(columns=names)
44 |     hic_chr.to_csv('matrix.txt',sep='\t', mode='a', index=None, header=None)
45 |     
46 | #===========================
47 | 


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