Metadata-Version: 1.1
Name: COVERnant
Version: 0.3.0
Summary: A tool to generate and manipulate coverage plots of high-throughput sequencing data.
Home-page: https://github.com/konrad/COVERnant
Author: Konrad U. Förstner
Author-email: konrad@foerstner.org
License: ISC License (ISCL)
Description: COVERnant
        =========
        
        COVERnant is a tool for the generation and manipulation of coverage
        files (currently in wiggle format) of high-throughput sequencing data.
        
        The tool is currently in an **early development stage**.
        
        COVERnant has several subcommands as its command line help shows:
        
        ::
        
            $ covernant -h
            usage: covernant [-h] [--version]
                             {ratio,extract,plot_matrix,bed_to_wig,rescale_wig} ...
        
            positional arguments:
              {ratio,extract,plot_matrix,bed_to_wig,rescale_wig}
                                    commands
                ratio               Generate ratio plots of two alignment files in Bam
                                    formar.
                extract             Extract coverage values from a wiggle file based on
                                    coordinates in a bed file and generate a matrix.
                plot_matrix         Plot the content of the extracted coverage matrix.
                bed_to_wig          Converts Bed files to coverage files in wiggle formats
                rescale_wig         Multiplies each value of a wiggle file with a given
                                    factor.
        
            optional arguments:
              -h, --help            show this help message and exit
              --version, -v         show version
        
        Subcommand ``ratio``
        --------------------
        
        ::
        
            usage: covernant ratio [-h] [--denominator DENOMINATOR_BAM_FILE]
                                   [--numerator NUMERATOR_BAM_FILE]
                                   [--output_prefix OUTPUT_PREFIX] [--paired_end]
                                   [--window_size WINDOW_SIZE] [--step_size STEP_SIZE]
                                   [--factor_numerator FACTOR_NUMERATOR]
                                   [--factor_denominator FACTOR_DENOMINATOR]
                                   [--keep_zero_coverage]
                                   [--denominator_name DENOMINATOR_NAME]
                                   [--numerator_name NUMERATOR_NAME]
                                   [--ratio_name RATIO_NAME]
        
            optional arguments:
              -h, --help            show this help message and exit
              --denominator DENOMINATOR_BAM_FILE
              --numerator NUMERATOR_BAM_FILE
              --output_prefix OUTPUT_PREFIX, -o OUTPUT_PREFIX
              --paired_end          Paired reads are treated as one fragment an the start
                                    and end positions are used accordingly
              --window_size WINDOW_SIZE
                                    Window size for sliding window average calculation.
                                    Must be an odd number. (Default is 1).
              --step_size STEP_SIZE
                                    Step size for sliding window average calculation.
                                    Default is 1.
              --factor_numerator FACTOR_NUMERATOR
                                    A factor the numerator values are are multiplied with.
              --factor_denominator FACTOR_DENOMINATOR
                                    A factor the denominator values are are multiplied
                                    with.
              --keep_zero_coverage  Also write coordinates that have a coverage of 0.
                                    Default is to discard those.
              --denominator_name DENOMINATOR_NAME
              --numerator_name NUMERATOR_NAME
              --ratio_name RATIO_NAME
        
        Subcommand ``extract``
        ----------------------
        
        ::
        
            $ covernant extract -h
            usage: covernant extract [-h] [--output_prefix OUTPUT_PREFIX]
                                     [--flip_reverse_strand]
                                     [--matrix_alignment {left,center,right}]
                                     [--window_size WINDOW_SIZE] [--step_size STEP_SIZE]
                                     coverage_file coordinate_file
        
            positional arguments:
              coverage_file
              coordinate_file
        
            optional arguments:
              -h, --help            show this help message and exit
              --output_prefix OUTPUT_PREFIX
              --flip_reverse_strand
                                    Flip the coverage value list of entries located at the
                                    minus strand
              --matrix_alignment {left,center,right}
                                    default is 'left'.
              --window_size WINDOW_SIZE
                                    Window size for sliding window average calculation.
                                    Must be an odd number.
              --step_size STEP_SIZE
                                    Step size for sliding window average calculation.
                                    Default is 1.
        
        Subcommand ``plot_matrix``
        --------------------------
        
        ::
        
            $ covernant plot_matrix -h
            usage: covernant plot_matrix [-h] [--output_file OUTPUT_FILE]
                                         [--share_x_range] [--share_y_max]
                                         matrix_file
        
            positional arguments:
              matrix_file
        
            optional arguments:
              -h, --help            show this help message and exit
              --output_file OUTPUT_FILE
              --share_x_range       Use the same x range in all plots.
              --share_y_max         Use the same maximum y value in all plots.
        
        Subcommand ``bed_to_wig``
        -------------------------
        
        ::
        
            $ covernant bed_to_wig -h
            usage: covernant bed_to_wig [-h] [--output_prefix OUTPUT_PREFIX]
                                        [--window_size WINDOW_SIZE]
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: ISC License (ISCL)
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
