A tool to generate and manipulate coverage plots of high-throughput sequencing data.
Project description
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 usage: covernant [-h] [--version] {ratio,extract,plot_matrix,bed_to_wig} ... positional arguments: {ratio,extract,plot_matrix,bed_to_wig} commands ratio Generate ratio plots of two alignment files. extract Extract coverage values from wiggle file. plot_matrix Plot the content of the extracted coverage matrix. bed_to_wig Converts Bed file to coverage in wiggle formats optional arguments: -h, --help show this help message and exit --version, -v show version
Subcommand ratio
$ covernant ratio -h usage: covernant ratio [-h] [--output OUTPUT_PREFIX] [--paired_end] [--window_size WINDOW_SIZE] [--step_size STEP_SIZE] [--factor FACTOR] [--keep_zero_coverage] [--denominator_name DENOMINATOR_NAME] [--numerator_name NUMERATOR_NAME] [--ratio_name RATIO_NAME] denominator_bam_file numerator_bam_file positional arguments: denominator_bam_file numerator_bam_file optional arguments: -h, --help show this help message and exit --output 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 FACTOR A factor the final ratio is 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]
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