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