Mercurial > repos > mheinzl > variant_analyzer2

comparison read2mut.py @ 17:f06067bedfc5 draft

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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Mon, 22 Feb 2021 14:40:07 +0000
parents 30aec05d04d3
children d910b6dfd826
comparison
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16:30aec05d04d3 17:f06067bedfc5
61 help='Integer threshold for Phred score. Only reads higher than this threshold are considered. Default 20.') 61 help='Integer threshold for Phred score. Only reads higher than this threshold are considered. Default 20.')
62 parser.add_argument('--trim', type=int, default=10, 62 parser.add_argument('--trim', type=int, default=10,
63 help='Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10.') 63 help='Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10.')
64 parser.add_argument('--chimera_correction', action="store_true", 64 parser.add_argument('--chimera_correction', action="store_true",
65 help='Count chimeric variants and correct the variant frequencies') 65 help='Count chimeric variants and correct the variant frequencies')
66 parser.add_argument('--delim_csv', type=str, default=",",
67 help='Delimiter in csv summary file. Default comma.')
68
69
70 return parser 66 return parser
71 67
72 68
73 def safe_div(x, y): 69 def safe_div(x, y):
74 if y == 0: 70 if y == 0:
236 pure_tags_dict_short[key] = value 232 pure_tags_dict_short[key] = value
237 else: 233 else:
238 pure_tags_dict_short = pure_tags_dict 234 pure_tags_dict_short = pure_tags_dict
239 235
240 csv_data = open(outputFile_csv, "w") 236 csv_data = open(outputFile_csv, "w")
241 csv_writer = csv.writer(csv_data, delimiter=delim_csv) 237 csv_writer = csv.writer(csv_data, delimiter=",")
242 238
243 # output summary with threshold 239 # output summary with threshold
244 workbook = xlsxwriter.Workbook(outfile) 240 workbook = xlsxwriter.Workbook(outfile)
245 workbook2 = xlsxwriter.Workbook(outfile2) 241 workbook2 = xlsxwriter.Workbook(outfile2)
246 workbook3 = xlsxwriter.Workbook(outfile3) 242 workbook3 = xlsxwriter.Workbook(outfile3)