kopardev/clipperhelper

Scripts to create custom references to be used with clipper

• clipperhelper
  • pre-requisites
  • usage
  • example
  • comments etc.

clipperhelper

Script to create files required to run clipper on custom references.

pre-requisites

clipperhelper only needs pandas and argparse python libraries. Details provided in the requirements.txt file, if you wish to create a conda environment.

usage

% python clipperhelper/util/make_custom_species_files.py --help
usage: make_custom_species_files.py [-h] --gtf GTF --species SPECIES

Create clipper input files for custom species

optional arguments:
  -h, --help         show this help message and exit
  --gtf GTF          input GTF file
  --species SPECIES  species name to be used as output file prefix

example

% python clipperhelper/util/make_custom_species_files.py --gtf hg19+virus.gtf --species hybrid

The above command will create the following files:

• hybrid_genes.bed
• hybrid_exons.bed
• hybrid.AS.STRUCTURE.COMPILED.gff

All of these are required to run clipper on a custom genome with customized annotations (GTF).

comments etc.

Feel free to contact me at vishal.koparde@nih.gov