Mercurial > repos > geoffrey.dintilhac > bam_to_bed

comparison bamtobed.py @ 0:68f7b5a4b1e2 draft

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author geoffrey.dintilhac
date Sat, 21 Dec 2019 12:56:50 -0500
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-1:000000000000 0:68f7b5a4b1e2
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
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55