comparison snp_wind.py @ 0:e958c5f7c9d1 draft

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author greg
date Wed, 22 Nov 2023 15:34:14 +0000
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-1:000000000000 0:e958c5f7c9d1
1 #!/usr/bin/env python
2
3 import argparse
4 import os
5 from os.path import join as j
6 from itertools import zip_longest
7
8
9 def setup(base_dir, names=[], fwds=[], revs=[], extension='vcf', pattern="{name}.{orient}.{ext}"):
10 if fwds and revs and names and len(fwds) != len(revs) != len(names):
11 raise ValueError('number of forward reads must equal number of reverse reads and names')
12 elif len(fwds) != len(names) or not fwds or not names:
13 raise ValueError('number of forward reads must equal number of names')
14 with open(j(base_dir, 'snp-unwind.sh'), 'w') as unwind:
15 for i, (name, fwd, rev) in enumerate(zip_longest(names, fwds, revs)):
16 dir = j(base_dir, str(i))
17 sample_dir = j(dir, name)
18 os.makedirs(sample_dir)
19 target_f = j(sample_dir, pattern.format(name=name, orient=1, ext=extension))
20 if rev:
21 target_r = j(sample_dir, pattern.format(name=name, orient=2, ext=extension))
22 os.symlink(fwd, target_f)
23 if rev:
24 os.symlink(rev, target_r)
25 print(sample_dir)
26 if rev:
27 unwind.write('unlink {}\n'.format(target_r))
28 unwind.write('unlink {}\n'.format(target_f))
29 unwind.write('rmdir {}\n'.format(sample_dir))
30 unwind.write('rmdir {}\n'.format(dir))
31
32
33 if __name__ == '__main__':
34 parser = argparse.ArgumentParser(description="set up vcf symlink directories for snp-pipeline")
35 parser.add_argument('base_dir')
36 parser.add_argument('-n', dest='names', type=str, action='append', default=[])
37 parser.add_argument('-f', dest='fwds', type=str, action='append', default=[])
38 parser.add_argument('-r', dest='revs', type=str, action='append', default=[])
39 parser.add_argument('-e', dest='extension', default='vcf')
40 parser.add_argument('-p', dest='pattern', default='{name}.{orient}.{ext}')
41 params = parser.parse_args()
42 setup(**vars(params))