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

mkarv {{VERSION}}                                  April 2024                                           MKARV(1)