Mercurial > repos > iuc > filter_tabular
diff filter_tabular.py @ 0:6fbd9d25ceef draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
author | iuc |
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date | Tue, 18 Jul 2017 09:06:47 -0400 |
parents | |
children | 4d5aae46f850 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_tabular.py Tue Jul 18 09:06:47 2017 -0400 @@ -0,0 +1,68 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import json +import optparse +import os.path +import sys + +from filters import filter_file + + +def __main__(): + # Parse Command Line + parser = optparse.OptionParser() + parser.add_option('-i', '--input', dest='input', default=None, + help='Input file for filtering') + parser.add_option('-j', '--jsonfile', dest='jsonfile', default=None, + help='JSON array of filter specifications') + parser.add_option('-o', '--output', dest='output', default=None, + help='Output file for query results') + parser.add_option('-v', '--verbose', dest='verbose', default=False, + action='store_true', + help='verbose') + (options, args) = parser.parse_args() + + if options.input is not None: + try: + inputPath = os.path.abspath(options.input) + inputFile = open(inputPath, 'r') + except Exception as e: + exit('Error: %s' % (e)) + else: + inputFile = sys.stdin + + if options.output is not None: + try: + outputPath = os.path.abspath(options.output) + outputFile = open(outputPath, 'w') + except Exception as e: + exit('Error: %s' % (e)) + else: + outputFile = sys.stdout + + filters = None + if options.jsonfile: + try: + with open(options.jsonfile) as fh: + filters = json.load(fh) + except Exception as e: + exit('Error: %s' % (e)) + + if options.verbose and filters: + for f in filters: + print('%s %s' % (f['filter'], + ', '.join( + ['%s: %s' % (k, f[k]) + for k in set(f.keys()) - set(['filter'])])), + file=sys.stdout) + + try: + filter_file(inputFile, outputFile, filters=filters) + except Exception as e: + exit('Error: %s' % (e)) + + +if __name__ == "__main__": + __main__()