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