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                       -- all your genes belong to us!

GeFComp is a Python script for comparing performance metrics of different gene finding tools. Given a number of [genome assemblies] ga-wiki in FASTA format, GeFComp executes each available tool on each of the genomes and evaluates Type I and Type II errors, also known as false positives and false negatives. Results are then summarised

Currently, GeFComp supports:

  • [GeneMark] gm
  • [GeneMark.hmm] gm
  • [GeneMark-S] gm

Installation

Python-only requirements can be installed via the usual pip boilerplate, but to do the evaluation you also have to make sure that the following tools are available in $PATH:

  • BWA bwa, a popular short read aligner.
$ pip install -r requirements.txt

Or, if you prefer Debian and system-wide installation:

# aptitude install python-biopython bwa

Usage

$ gefcomp.py config.py
$ ls *.csv
summary.csv