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comparison find_in_reference.py @ 1:856033fb26e8

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Add case insensitive option
author Jim Johnson <jj@umn.edu>
date Fri, 17 Jan 2014 14:50:53 -0600
parents fe0327a3ba81
children 30975b3ff0dc
comparison
equal deleted inserted replaced
0:fe0327a3ba81 1:856033fb26e8
38 parser.add_option( '-r', '--reference', dest='reference', help='The reference file to filter against' ) 38 parser.add_option( '-r', '--reference', dest='reference', help='The reference file to filter against' )
39 parser.add_option( '-o', '--output', dest='output', help='The output file for input lines filtered by reference') 39 parser.add_option( '-o', '--output', dest='output', help='The output file for input lines filtered by reference')
40 parser.add_option( '-f', '--filtered', dest='filtered', help='The output file for input lines not in the output') 40 parser.add_option( '-f', '--filtered', dest='filtered', help='The output file for input lines not in the output')
41 parser.add_option('-c','--input_column', dest='input_column', default=None, help='The column for the value in the input file. (first column = 1, default to last column)') 41 parser.add_option('-c','--input_column', dest='input_column', default=None, help='The column for the value in the input file. (first column = 1, default to last column)')
42 parser.add_option('-C','--reference_column', dest='reference_column', default=None, help='The column for the value in the reference file. (first column = 1, default to last column)') 42 parser.add_option('-C','--reference_column', dest='reference_column', default=None, help='The column for the value in the reference file. (first column = 1, default to last column)')
43 parser.add_option( '-I', '--case_insensitive', dest='ignore_case', action="store_true", default=False, help='case insensitive' )
43 parser.add_option( '-k', '--keep', dest='keep', action="store_true", default=False, help='' ) 44 parser.add_option( '-k', '--keep', dest='keep', action="store_true", default=False, help='' )
44 parser.add_option( '-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout' ) 45 parser.add_option( '-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout' )
45 (options, args) = parser.parse_args() 46 (options, args) = parser.parse_args()
46 # Input files 47 # Input files
47 if options.input != None: 48 if options.input != None:
87 refFile = None 88 refFile = None
88 for ln,line in enumerate(inputFile): 89 for ln,line in enumerate(inputFile):
89 try: 90 try:
90 found = False 91 found = False
91 search_string = line.split('\t')[incol].rstrip('\r\n') 92 search_string = line.split('\t')[incol].rstrip('\r\n')
93 if options.ignore_case:
94 search_string = search_string.upper()
92 if options.debug: 95 if options.debug:
93 print >> sys.stderr, "search: %s" % (search_string) 96 print >> sys.stderr, "search: %s" % (search_string)
94 refFile = open(options.reference,'r') 97 refFile = open(options.reference,'r')
95 for tn,fline in enumerate(refFile): 98 for tn,fline in enumerate(refFile):
96 target_string = fline.split('\t')[refcol] 99 target_string = fline.split('\t')[refcol]
100 if options.ignore_case:
101 target_string = target_string.upper()
97 if options.debug: 102 if options.debug:
98 print >> sys.stderr, "in: %s %s %s" % (search_string,search_string in target_string,target_string) 103 print >> sys.stderr, "in: %s %s %s" % (search_string,search_string in target_string,target_string)
99 if search_string in target_string: 104 if search_string in target_string:
100 found = True 105 found = True
101 break 106 break