Mercurial > repos > iuc > gemini_qc
annotate test-data/util/shrink_tabix.py @ 7:86e46972e183 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
| author | iuc |
|---|---|
| date | Tue, 10 Mar 2020 06:14:22 -0400 |
| parents | 246ad1a7ff20 |
| children |
| rev | line source |
|---|---|
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4
246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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1 from __future__ import print_function |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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2 |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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3 import argparse |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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4 |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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5 import pysam |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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6 |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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7 |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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8 def main(infile, ofile, region): |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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9 print(infile, '->', ofile) |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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10 with pysam.Tabixfile(infile) as i: |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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11 fformat = i.format.lower() |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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12 if fformat == 'sam': |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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13 fformat = 'bed' |
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246ad1a7ff20
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': |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
15 ofile = ofile[:-3] |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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16 with open(ofile, 'w') as o: |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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17 try: |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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18 region_it = i.fetch(region=region) |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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19 except ValueError: |
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246ad1a7ff20
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) |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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21 for line in i.header: |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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22 o.write(line + '\n') |
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246ad1a7ff20
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: |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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24 o.write(str(line) + '\n') |
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246ad1a7ff20
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) |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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26 |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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27 |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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28 if __name__ == '__main__': |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
29 p = argparse.ArgumentParser() |
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246ad1a7ff20
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') |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
31 p.add_argument( |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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32 '-r', '--region', |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
33 required=True, |
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246ad1a7ff20
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' |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
35 ) |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
36 p.add_argument( |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
37 '-o', '--ofile', |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
38 required=True, |
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246ad1a7ff20
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" |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
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40 ) |
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246ad1a7ff20
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()) |
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246ad1a7ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents:
diff
changeset
|
42 main(**args) |