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comparison fsd.py @ 5:69f47e0b804e draft

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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit 9829d657c07703b117bed2f259ddba432b244312
author mheinzl
date Wed, 09 May 2018 09:13:46 -0400
parents 648d5df50ca8
children c4b8222dce29
comparison
equal deleted inserted replaced
4:5bae51dc7fa1 5:69f47e0b804e
27 data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter='\t', comments='#', dtype='string') 27 data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter='\t', comments='#', dtype='string')
28 return(data_array) 28 return(data_array)
29 29
30 def make_argparser(): 30 def make_argparser():
31 parser = argparse.ArgumentParser(description='Family Size Distribution of duplex sequencing data') 31 parser = argparse.ArgumentParser(description='Family Size Distribution of duplex sequencing data')
32 parser.add_argument('inputFile', 32 # parser.add_argument('inputFile',
33 help='Tabular File with three columns: ab or ba, tag and family size.') 33 # help='Tabular File with three columns: ab or ba, tag and family size.')
34 parser.add_argument('--inputName1') 34 parser.add_argument('--inputName1')
35 parser.add_argument('--inputFile2',default=None, 35 parser.add_argument('--inputFile2',default=None,
36 help='Tabular File with three columns: ab or ba, tag and family size.') 36 help='Tabular File with three columns: ab or ba, tag and family size.')
37 parser.add_argument('--inputName2') 37 parser.add_argument('--inputName2')
38 parser.add_argument('--inputFile3',default=None, 38 parser.add_argument('--inputFile3',default=None,
51 51
52 def compare_read_families(argv): 52 def compare_read_families(argv):
53 parser = make_argparser() 53 parser = make_argparser()
54 args=parser.parse_args(argv[1:]) 54 args=parser.parse_args(argv[1:])
55 55
56 firstFile = args.inputFile 56 #firstFile = args.inputFile
57 name1 = args.inputName1 57 name1 = args.inputName1
58 firstFile = args.inputName1
59
58 secondFile = args.inputFile2 60 secondFile = args.inputFile2
59 name2 = args.inputName2 61 name2 = args.inputName2
60 thirdFile = args.inputFile3 62 thirdFile = args.inputFile3
61 name3 = args.inputName3 63 name3 = args.inputName3
62 fourthFile = args.inputFile4 64 fourthFile = args.inputFile4