Mercurial > repos > iuc > query_tabular
comparison filter_tabular.py @ 0:3708ff0198b7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
| author | iuc |
|---|---|
| date | Tue, 18 Jul 2017 09:07:07 -0400 |
| parents | |
| children | cf34c344508d |
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| -1:000000000000 | 0:3708ff0198b7 |
|---|---|
| 1 #!/usr/bin/env python | |
| 2 | |
| 3 from __future__ import print_function | |
| 4 | |
| 5 import json | |
| 6 import optparse | |
| 7 import os.path | |
| 8 import sys | |
| 9 | |
| 10 from filters import filter_file | |
| 11 | |
| 12 | |
| 13 def __main__(): | |
| 14 # Parse Command Line | |
| 15 parser = optparse.OptionParser() | |
| 16 parser.add_option('-i', '--input', dest='input', default=None, | |
| 17 help='Input file for filtering') | |
| 18 parser.add_option('-j', '--jsonfile', dest='jsonfile', default=None, | |
| 19 help='JSON array of filter specifications') | |
| 20 parser.add_option('-o', '--output', dest='output', default=None, | |
| 21 help='Output file for query results') | |
| 22 parser.add_option('-v', '--verbose', dest='verbose', default=False, | |
| 23 action='store_true', | |
| 24 help='verbose') | |
| 25 (options, args) = parser.parse_args() | |
| 26 | |
| 27 if options.input is not None: | |
| 28 try: | |
| 29 inputPath = os.path.abspath(options.input) | |
| 30 inputFile = open(inputPath, 'r') | |
| 31 except Exception as e: | |
| 32 exit('Error: %s' % (e)) | |
| 33 else: | |
| 34 inputFile = sys.stdin | |
| 35 | |
| 36 if options.output is not None: | |
| 37 try: | |
| 38 outputPath = os.path.abspath(options.output) | |
| 39 outputFile = open(outputPath, 'w') | |
| 40 except Exception as e: | |
| 41 exit('Error: %s' % (e)) | |
| 42 else: | |
| 43 outputFile = sys.stdout | |
| 44 | |
| 45 filters = None | |
| 46 if options.jsonfile: | |
| 47 try: | |
| 48 with open(options.jsonfile) as fh: | |
| 49 filters = json.load(fh) | |
| 50 except Exception as e: | |
| 51 exit('Error: %s' % (e)) | |
| 52 | |
| 53 if options.verbose and filters: | |
| 54 for f in filters: | |
| 55 print('%s %s' % (f['filter'], | |
| 56 ', '.join( | |
| 57 ['%s: %s' % (k, f[k]) | |
| 58 for k in set(f.keys()) - set(['filter'])])), | |
| 59 file=sys.stdout) | |
| 60 | |
| 61 try: | |
| 62 filter_file(inputFile, outputFile, filters=filters) | |
| 63 except Exception as e: | |
| 64 exit('Error: %s' % (e)) | |
| 65 | |
| 66 | |
| 67 if __name__ == "__main__": | |
| 68 __main__() |