CLI Reference

References of how to use the command line interface of the program and notes on some ways particular commands work that could trip you up.

General help message is as follows:

usage: hlsmallrna [-h] [-q] [-C PATH_TO_CONFIG]
                {process,sort,extractnc,unitas,targetid,all} ...

Pipeline to process small RNAs

positional arguments:
  {process,sort,extractnc,unitas,targetid,all}
    process             Preprocessing for the RNA
    sort                Find RNAs that align to a genome and sort them by
                        length
    extractnc           Extract the noncoding region from a fasta with a GFF
                        file
    unitas              Run unitas on split files and merge results
    targetid            Align small RNA to a number of genome features to find
                        out what is targeted
    all                 Run process, sort and unitas one after the other

optional arguments:
  -h, --help            show this help message and exit
  -q, --quiet           Suppress output from intermediate commands
  -C PATH_TO_CONFIG, --path-to-config PATH_TO_CONFIG
                        Path to the TOML format config file to use