Mercurial > repos > fubar > jbrowse2

comparison maf2bed.py @ 61:e7a6f7a7148d draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty
author fubar
date Tue, 26 Mar 2024 00:52:34 +0000
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children b1260bca5fdc
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60:81d535970196 61:e7a6f7a7148d
1 #!/usr/bin/env python
2 # painfully converted from b0rken perl from
3 # https://unpkg.com/browse/jbrowse-plugin-mafviewer@1.0.6/dist/
4 # license is Apache2_license.txt included here
5
6 import sys
7
8 id = 0
9 buffer = ''
10 start = 0
11 end = 0
12 score = 0
13 chrom = ''
14
15 db = "%s." % sys.argv[1]
16 # Read input from stdin
17 for line in sys.stdin:
18 line = line.strip()
19 if not line:
20 continue
21
22 line = line.split()
23 if line[0] == 's' and line[1].startswith(db):
24 chrom = line[1]
25 chrom = chrom.replace(db, '')
26 start = int(line[2])
27 end = int(line[2]) + int(line[3])
28 line = line[1:]
29 line = ':'.join(line)
30 temp = line
31 buffer = temp if buffer == '' else f"{buffer},{temp}"
32 elif line[0] == 'a':
33 score = int(line[1].split('=')[1])
34 if id > 0:
35 sys.stdout.write('\t'.join([chrom, '%d' % start, '%d' % end, f"{sys.argv[1]}_{id}", '%d' % score, buffer])+ '\n')
36 id += 1
37 buffer = ''
38 elif line[0] == 's':
39 line = line[1:]
40 line = ':'.join(line)
41 temp = line
42 buffer = temp if buffer == '' else f"{buffer},{temp}"
43
44 sys.stdout.write('\t'.join([chrom, '%d' % start, '%d' % end, f"{sys.argv[1]}_{id}", '%d' % score, buffer]) + '\n')