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        "author": "Konrad U. F\u00f6rstner",
        "author_email": "konrad@foerstner.org",
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        "classifiers": [
            "License :: OSI Approved :: ISC License (ISCL)",
            "Operating System :: POSIX",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "COVERnant\n=========\n\nCOVERnant is a tool for the generation and manipulation of coverage\nfiles (currently in wiggle format) of high-throughput sequencing data.\n\nThe tool is currently in an **early development stage**.\n\nCOVERnant has several subcommands as its command line help shows:\n\n::\n\n    $ covernant -h\n    usage: covernant [-h] [--version]\n                     {ratio,extract,plot_matrix,bed_to_wig,rescale_wig} ...\n\n    positional arguments:\n      {ratio,extract,plot_matrix,bed_to_wig,rescale_wig}\n                            commands\n        ratio               Generate ratio plots of two alignment files in Bam\n                            formar.\n        extract             Extract coverage values from a wiggle file based on\n                            coordinates in a bed file and generate a matrix.\n        plot_matrix         Plot the content of the extracted coverage matrix.\n        bed_to_wig          Converts Bed files to coverage files in wiggle formats\n        rescale_wig         Multiplies each value of a wiggle file with a given\n                            factor.\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      --version, -v         show version\n\nSubcommand ``ratio``\n--------------------\n\n::\n\n    usage: covernant ratio [-h] [--denominator DENOMINATOR_BAM_FILE]\n                           [--numerator NUMERATOR_BAM_FILE]\n                           [--output_prefix OUTPUT_PREFIX] [--paired_end]\n                           [--window_size WINDOW_SIZE] [--step_size STEP_SIZE]\n                           [--factor_numerator FACTOR_NUMERATOR]\n                           [--factor_denominator FACTOR_DENOMINATOR]\n                           [--keep_zero_coverage]\n                           [--denominator_name DENOMINATOR_NAME]\n                           [--numerator_name NUMERATOR_NAME]\n                           [--ratio_name RATIO_NAME]\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      --denominator DENOMINATOR_BAM_FILE\n      --numerator NUMERATOR_BAM_FILE\n      --output_prefix OUTPUT_PREFIX, -o OUTPUT_PREFIX\n      --paired_end          Paired reads are treated as one fragment an the start\n                            and end positions are used accordingly\n      --window_size WINDOW_SIZE\n                            Window size for sliding window average calculation.\n                            Must be an odd number. (Default is 1).\n      --step_size STEP_SIZE\n                            Step size for sliding window average calculation.\n                            Default is 1.\n      --factor_numerator FACTOR_NUMERATOR\n                            A factor the numerator values are are multiplied with.\n      --factor_denominator FACTOR_DENOMINATOR\n                            A factor the denominator values are are multiplied\n                            with.\n      --keep_zero_coverage  Also write coordinates that have a coverage of 0.\n                            Default is to discard those.\n      --denominator_name DENOMINATOR_NAME\n      --numerator_name NUMERATOR_NAME\n      --ratio_name RATIO_NAME\n\nSubcommand ``extract``\n----------------------\n\n::\n\n    $ covernant extract -h\n    usage: covernant extract [-h] [--output_prefix OUTPUT_PREFIX]\n                             [--flip_reverse_strand]\n                             [--matrix_alignment {left,center,right}]\n                             [--window_size WINDOW_SIZE] [--step_size STEP_SIZE]\n                             coverage_file coordinate_file\n\n    positional arguments:\n      coverage_file\n      coordinate_file\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      --output_prefix OUTPUT_PREFIX\n      --flip_reverse_strand\n                            Flip the coverage value list of entries located at the\n                            minus strand\n      --matrix_alignment {left,center,right}\n                            default is 'left'.\n      --window_size WINDOW_SIZE\n                            Window size for sliding window average calculation.\n                            Must be an odd number.\n      --step_size STEP_SIZE\n                            Step size for sliding window average calculation.\n                            Default is 1.\n\nSubcommand ``plot_matrix``\n--------------------------\n\n::\n\n    $ covernant plot_matrix -h\n    usage: covernant plot_matrix [-h] [--output_file OUTPUT_FILE]\n                                 [--share_x_range] [--share_y_max]\n                                 matrix_file\n\n    positional arguments:\n      matrix_file\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      --output_file OUTPUT_FILE\n      --share_x_range       Use the same x range in all plots.\n      --share_y_max         Use the same maximum y value in all plots.\n\nSubcommand ``bed_to_wig``\n-------------------------\n\n::\n\n    $ covernant bed_to_wig -h\n    usage: covernant bed_to_wig [-h] [--output_prefix OUTPUT_PREFIX]\n                                [--window_size WINDOW_SIZE]",
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