Mercurial > repos > iuc > gemini_amend
comparison test-data/util/shrink_tabix.py @ 4:a02cd62adb70 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
| author | iuc |
|---|---|
| date | Fri, 14 Dec 2018 12:47:55 -0500 |
| parents | |
| children |
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| 3:4bd4870ecd33 | 4:a02cd62adb70 |
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| 1 from __future__ import print_function | |
| 2 | |
| 3 import argparse | |
| 4 | |
| 5 import pysam | |
| 6 | |
| 7 | |
| 8 def main(infile, ofile, region): | |
| 9 print(infile, '->', ofile) | |
| 10 with pysam.Tabixfile(infile) as i: | |
| 11 fformat = i.format.lower() | |
| 12 if fformat == 'sam': | |
| 13 fformat = 'bed' | |
| 14 if ofile[-3:] == '.gz': | |
| 15 ofile = ofile[:-3] | |
| 16 with open(ofile, 'w') as o: | |
| 17 try: | |
| 18 region_it = i.fetch(region=region) | |
| 19 except ValueError: | |
| 20 region_it = i.fetch(region='chr' + region) | |
| 21 for line in i.header: | |
| 22 o.write(line + '\n') | |
| 23 for line in region_it: | |
| 24 o.write(str(line) + '\n') | |
| 25 pysam.tabix_index(ofile, preset=fformat, force=True) | |
| 26 | |
| 27 | |
| 28 if __name__ == '__main__': | |
| 29 p = argparse.ArgumentParser() | |
| 30 p.add_argument('infile') | |
| 31 p.add_argument( | |
| 32 '-r', '--region', | |
| 33 required=True, | |
| 34 help='the region of the input file to rewrite' | |
| 35 ) | |
| 36 p.add_argument( | |
| 37 '-o', '--ofile', | |
| 38 required=True, | |
| 39 help="the name of the output file" | |
| 40 ) | |
| 41 args = vars(p.parse_args()) | |
| 42 main(**args) |