|
0
|
1 #!/usr/bin/env python
|
|
|
2
|
|
|
3 import argparse
|
|
|
4 import os
|
|
|
5
|
|
|
6 parser = argparse.ArgumentParser(description='Call bamtobed with parameters')
|
|
|
7 parser.add_argument('-i', '--inputBAM', required=True, help='input BAM file')
|
|
|
8 parser.add_argument('-o', '--outputBED', required=True, help='output BED file')
|
|
|
9 parser.add_argument('-oot', '--otherOutputType', required=True, help='Y or N')
|
|
|
10 parser.add_argument('-f', '--outputFormat', required=False, help='output file format')
|
|
|
11 parser.add_argument('-sc', '--scoreCalculation', required=True, help='calculation for BED score')
|
|
|
12 parser.add_argument('-tag', '--tag', required=False, help='another tag')
|
|
|
13 parser.add_argument('-spt', '--splitD', required=False, help='split : with "N" CIGAR and "D" operation', action="store_true")
|
|
|
14 parser.add_argument('-cgr', '--cigar', required=False, help='cigar string', action="store_true")
|
|
|
15
|
|
|
16 args = parser.parse_args()
|
|
|
17
|
|
|
18 # Displays the other output format if selected.
|
|
|
19 if args.otherOutputType == "Y":
|
|
|
20 print('format output chosen : ' + args.outputFormat)
|
|
|
21
|
|
|
22 # Construction of the command line calling the tool.
|
|
|
23 myCommandLine = ('bedtools bamtobed'+' -i ' + args.inputBAM)
|
|
|
24
|
|
|
25 # Other output format options.
|
|
|
26 if args.otherOutputType == "Y":
|
|
|
27 if args.outputFormat == "BEDPE":
|
|
|
28 myCommandLine += (' -bedpe ')
|
|
|
29 elif args.outputFormat == "BED12":
|
|
|
30 myCommandLine += (' -bed12 ')
|
|
|
31
|
|
|
32 # Score calculation options.
|
|
|
33 if args.scoreCalculation == "ed":
|
|
|
34 myCommandLine += (' -ed ')
|
|
|
35 elif args.scoreCalculation == "tag":
|
|
|
36 myCommandLine += (' -tag ' + args.tag)
|
|
|
37
|
|
|
38 # Split option.
|
|
|
39 if args.splitD:
|
|
|
40 myCommandLine += (' -splitD ')
|
|
|
41 print('Splitted BAM')
|
|
|
42
|
|
|
43 # CIGAR option.
|
|
|
44 if args.cigar:
|
|
|
45 myCommandLine += (' -cigar ')
|
|
|
46 print('CIGAR string column added')
|
|
|
47
|
|
|
48 myCommandLine += (' > ' + args.outputBED)
|
|
|
49
|
|
|
50 # Running of the command line.
|
|
|
51 os.system(myCommandLine)
|
|
|
52
|
|
|
53
|
|
|
54
|
|
|
55
|
