Mercurial > hg > Lemuriformes
comparison lemuriformes/issubset.py @ 15:0d1b8bb1d97b
SQL + data related functionality
| author | Jeff Hammel <k0scist@gmail.com> |
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| date | Sun, 10 Dec 2017 17:16:52 -0800 |
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| children |
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| 14:756dbd3e391e | 15:0d1b8bb1d97b |
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| 1 #!/usr/bin/env python | |
| 2 # -*- coding: utf-8 -*- | |
| 3 | |
| 4 """ | |
| 5 determine if one CSV column is a subsset of another. | |
| 6 If it is a subset, output nothing and exit 0. | |
| 7 If it is not a subset, output all elements that are | |
| 8 in the asserted subset but not the total set | |
| 9 and exits 1. | |
| 10 Exits 2 on error. | |
| 11 """ | |
| 12 | |
| 13 import os | |
| 14 import sys | |
| 15 from collections import OrderedDict | |
| 16 from .cli import ConfigurationParser | |
| 17 from .uniques import uniques | |
| 18 | |
| 19 def main(args=sys.argv[1:]): | |
| 20 """CLI""" | |
| 21 | |
| 22 sets = OrderedDict([('subset', "the `PATH` to the CSV and `COLUMN` of the asserted subset"), | |
| 23 ('total', "the `PATH` to the CSV and `COLUMN` of the total set")]) | |
| 24 | |
| 25 # parse command line | |
| 26 parser = ConfigurationParser(description=__doc__) | |
| 27 for key, description in sets.items(): | |
| 28 parser.add_argument(key, nargs=2, | |
| 29 help=description) | |
| 30 options = parser.parse_args(args) | |
| 31 | |
| 32 # sanity | |
| 33 filenames = set() | |
| 34 for key in sets.keys(): | |
| 35 # - ensure the values are listw | |
| 36 setattr(options, key, list(getattr(options, key))) | |
| 37 value = getattr(options, key) | |
| 38 # - make files absolute | |
| 39 value[0] = os.path.realpath(value[0]) | |
| 40 # - ensure files exist | |
| 41 filename = value[0] | |
| 42 if not os.path.isfile(filename): | |
| 43 parser.error("Not a file: {}".format(filename)) | |
| 44 filenames.add(filename) | |
| 45 | |
| 46 # read the files | |
| 47 columns = {filename: uniques(filename) | |
| 48 for filename in filenames} | |
| 49 | |
| 50 # assert that the columns are in the files they have been ascribed to | |
| 51 for key in sets.keys(): | |
| 52 filename, column = getattr(options, key) | |
| 53 if column not in columns[filename]: | |
| 54 parser.error("Column '{}' not found in file '{}'".format(column, filename)) | |
| 55 | |
| 56 # calculate the difference | |
| 57 difference = columns[options.subset[0]][options.subset[1]].difference( | |
| 58 columns[options.total[0]][options.total[1]]) | |
| 59 if not difference: | |
| 60 return | |
| 61 print ("\n".join([str(i) for i in sorted(difference)])) | |
| 62 sys.exit(1) | |
| 63 | |
| 64 | |
| 65 if __name__ == '__main__': | |
| 66 main() |