Process featureCounts Output

This script processes the output files generated by featureCounts to a simpler (and smaller) counts matrix.

Usage

usage: process-featurecounts [-h] [-V] [-v {error,warning,info,debug}] [-r <re>] [-s <re>] [-e] [-i <n>] [-k <n,[n]>] <file>

Reformat featureCounts output files

positional arguments:
  <file>                input featureCounts file

optional arguments:
  -h, --help            show this help message and exit
  -V, --version         show program's version number and exit
  -v {error,warning,info,debug}, --verbose {error,warning,info,debug}
                        Set logging level (default debug)
  -r <re>, --id-regex <re>
                        row ID regular expression to use (default
                        "^([^.]+)\.\d+(.*)$")
  -s <re>, --sample-regex <re>
                        sample name regular expression to use (default
                        "^(.*)$")
  -e, --include-header  include header comments
  -i <n>, --id-col <n>  gene ID column (default 1)
  -k <n,[n]>, --skip <n,[n]>
                        comma-separated columns to skip (default 2,3,4,5,6)

Header & row ID Trimming

process-featurecounts trims both the header sample names and the gene IDs using the specified sample-regex and id-regex regular expressions. After matching, all captured groups are concatenated to yield the output.

Installation

Installation should be as simple as:

git clone https://github.com/alastair-droop/process-featurecounts.git
cd process-featurecounts
python setup.py install