mkarv - Turns ataqv results into a web app
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.
- 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)
- -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