Mercurial > repos > iuc > gemini_set_somatic
annotate test-data/util/shrink_tabix.py @ 9:ac980103c5a5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
| author | iuc |
|---|---|
| date | Wed, 13 Jul 2022 15:11:29 +0000 |
| parents | 97a9409dfd78 |
| children |
| rev | line source |
|---|---|
|
3
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
1 from __future__ import print_function |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
2 |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
3 import argparse |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
4 |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
5 import pysam |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
6 |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
7 |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
8 def main(infile, ofile, region): |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
9 print(infile, '->', ofile) |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
10 with pysam.Tabixfile(infile) as i: |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
11 fformat = i.format.lower() |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
12 if fformat == 'sam': |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
13 fformat = 'bed' |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
14 if ofile[-3:] == '.gz': |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
15 ofile = ofile[:-3] |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
16 with open(ofile, 'w') as o: |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
17 try: |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
18 region_it = i.fetch(region=region) |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
19 except ValueError: |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
20 region_it = i.fetch(region='chr' + region) |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
21 for line in i.header: |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
22 o.write(line + '\n') |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
23 for line in region_it: |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
24 o.write(str(line) + '\n') |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
25 pysam.tabix_index(ofile, preset=fformat, force=True) |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
26 |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
27 |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
28 if __name__ == '__main__': |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
29 p = argparse.ArgumentParser() |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
30 p.add_argument('infile') |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
31 p.add_argument( |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
32 '-r', '--region', |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
33 required=True, |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
34 help='the region of the input file to rewrite' |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
35 ) |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
36 p.add_argument( |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
37 '-o', '--ofile', |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
38 required=True, |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
39 help="the name of the output file" |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
40 ) |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
41 args = vars(p.parse_args()) |
|
97a9409dfd78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
42 main(**args) |