Mercurial > repos > mheinzl > fsd
comparison fsd.py @ 6:c4b8222dce29 draft
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit 1667d50b521325eea1eada1b16029b1ba1379c5f
| author | mheinzl |
|---|---|
| date | Wed, 09 May 2018 09:20:06 -0400 |
| parents | 69f47e0b804e |
| children | 43b16247c35a |
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| 5:69f47e0b804e | 6:c4b8222dce29 |
|---|---|
| 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('--inputFile1', |
| 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.inputFile1 |
| 57 name1 = args.inputName1 | 57 name1 = args.inputName1 |
| 58 firstFile = args.inputName1 | 58 #firstFile = args.inputName1 |
| 59 | 59 |
| 60 secondFile = args.inputFile2 | 60 secondFile = args.inputFile2 |
| 61 name2 = args.inputName2 | 61 name2 = args.inputName2 |
| 62 thirdFile = args.inputFile3 | 62 thirdFile = args.inputFile3 |
| 63 name3 = args.inputName3 | 63 name3 = args.inputName3 |