MKARV

NAME

mkarv - Turns ataqv results into a web app

DESCRIPTION

usage: mkarv [-h] [-c CONCURRENCY] [-d DESCRIPTION] [-f] [-i] [-l]

[-m MAXIMUM_FRAGMENT_LENGTH] [-p PEAK_REFERENCE] [-r REFERENCE] [-t TEMPLATE_DIRECTORY] [-v] [--version] directory [metrics ...]

Given one or more ataqv metrics files in JSON format, creates an instance of the ataqv result visualization tool. The web application is copied into the named directory, and the JSON results are translated for it. The resulting directory can be loaded into a web browser locally by opening the index.html file, or published with a web server like Apache or nginx.

positional arguments:

directory

The path to the directory where the web app will be created.

metrics

One or more ataqv metrics files in JSON format. (default: None)

options:

-h, --help

show this help message and exit

-c CONCURRENCY, --concurrency CONCURRENCY

The number of concurrent processes to use (default: 1). (default: 1)

-d DESCRIPTION, --description DESCRIPTION

A description for the viewer instance. (default: None)

-f, --force

Overwrite the output directory if it exists. (default: False)

-i, --indent

If indent is given, JSON output will be pretty-printed and indented. (default: False)

-l, --less-redundant

Produce a viewer with fewer metrics (metrics that are expected to be largely redundant will not be displayed. (default: False)

-m MAXIMUM_FRAGMENT_LENGTH, --maximum-fragment-length
MAXIMUM_FRAGMENT_LENGTH

The maximum fragment length for which the distance to the reference fragment length count distribution will be measured. (default: 1000)

-p PEAK_REFERENCE, --peak-reference PEAK_REFERENCE

A reference set of peak metrics to plot. The default value is "SRR891268", the peak metrics of that sample in the ATAC-seq paper, as generated with MACS2 in our pipeline. It can be specified as "calculate", in which case these metrics will be averaged from the given metrics. It can also be the name of a JSON file, which must contain an object with two keys, "cumulative_fraction_of_hqaa" and "cumulative_fraction_of_territory", the value of each being an array of fractions of high-quality autosomal alignments (HQAA) or total peak territory, respectively. A tab- or comma-separated value file may also be given, in which each line contains two fractions, of HQAA and peak territory. All of these arrays should represent values at percentiles from 1-100. (default: SRR891268)

-r REFERENCE, --reference REFERENCE

How to make the reference fragment length count distribution. The default value is "SRR891268", the fragment length distribution of that sample in the ATAC-seq paper. It can be specified as "calculate", in which case a distance will be calculated for each set of metrics from a reference distribution constructed from the rest of the given metrics. It can also be the name of a file containing a reference distribution. This file may be in JSON format, containing an object mapping fragment lengths to counts (e.g. "{0: 0, 1: 10, 2: 17}", or it may be a tab- or comma-separated value file in which each line contains a fragment length and count. It may (default: SRR891268)

-t TEMPLATE_DIRECTORY, --template-directory TEMPLATE_DIRECTORY

The location of the web app directory template. (default: auto)

-v, --verbose

Talk more. (default: False)

--version

show program’s version number and exit