comparison read2mut.py @ 17:f06067bedfc5 draft

planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

16:30aec05d04d3

                        help='Integer threshold for Phred score. Only reads higher than this threshold are considered. Default 20.')
    parser.add_argument('--trim', type=int, default=10,
                        help='Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10.')
    parser.add_argument('--chimera_correction', action="store_true",
                        help='Count chimeric variants and correct the variant frequencies')
    parser.add_argument('--delim_csv', type=str, default=",",
                        help='Delimiter in csv summary file. Default comma.')


    return parser


def safe_div(x, y):
    if y == 0:

                pure_tags_dict_short[key] = value
    else:
        pure_tags_dict_short = pure_tags_dict

    csv_data = open(outputFile_csv, "w")
    csv_writer = csv.writer(csv_data, delimiter=delim_csv)

    # output summary with threshold
    workbook = xlsxwriter.Workbook(outfile)
    workbook2 = xlsxwriter.Workbook(outfile2)
    workbook3 = xlsxwriter.Workbook(outfile3)

17:f06067bedfc5

                        help='Integer threshold for Phred score. Only reads higher than this threshold are considered. Default 20.')
    parser.add_argument('--trim', type=int, default=10,
                        help='Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10.')
    parser.add_argument('--chimera_correction', action="store_true",
                        help='Count chimeric variants and correct the variant frequencies')
    return parser


def safe_div(x, y):
    if y == 0:

                pure_tags_dict_short[key] = value
    else:
        pure_tags_dict_short = pure_tags_dict

    csv_data = open(outputFile_csv, "w")
    csv_writer = csv.writer(csv_data, delimiter=",")

    # output summary with threshold
    workbook = xlsxwriter.Workbook(outfile)
    workbook2 = xlsxwriter.Workbook(outfile2)
    workbook3 = xlsxwriter.Workbook(outfile3)