From 8b2d7accb3b0945879f8944a9da5ecad8f3e7ae6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Konrad=20F=C3=B6rstner?= Date: Sun, 26 Mar 2017 13:06:15 +0200 Subject: [PATCH] Update readme --- README.md | 41 ++++++++++------- README.rst | 130 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 155 insertions(+), 16 deletions(-) create mode 100644 README.rst diff --git a/README.md b/README.md index 1212c8b..3f936af 100644 --- a/README.md +++ b/README.md @@ -12,16 +12,21 @@ 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} ... +$ covernant -h +usage: covernant [-h] [--version] + {ratio,extract,plot_matrix,bed_to_wig,rescale_wig} ... positional arguments: - {ratio,extract,plot_matrix,bed_to_wig} + {ratio,extract,plot_matrix,bed_to_wig,rescale_wig} commands - ratio Generate ratio plots of two alignment files. - extract Extract coverage values from wiggle file. + 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 file to coverage in wiggle formats + 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 @@ -31,22 +36,22 @@ optional arguments: ## Subcommand `ratio` ``` -$ covernant ratio -h -usage: covernant ratio [-h] [--output OUTPUT_PREFIX] [--paired_end] +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 FACTOR] [--keep_zero_coverage] + [--factor_numerator FACTOR_NUMERATOR] + [--factor_denominator FACTOR_DENOMINATOR] + [--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 + --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 @@ -55,7 +60,11 @@ optional arguments: --step_size STEP_SIZE Step size for sliding window average calculation. Default is 1. - --factor FACTOR A factor the final ratio is multiplied with. + --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 diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..a3c0a44 --- /dev/null +++ b/README.rst @@ -0,0 +1,130 @@ +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]