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README.md

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README

Overview

gfftk is a toolkit to examine GFF files and extract specific entries. The core functions to parse GFF file can be used in own projects. A simple example is given in the examples directory.

Currently ongoing

  • Implementing the extraction of specific entries directly from the source FASTA file
  • Code documentation

Requirements

  • GCC >= 9.0.0

Build

$: git clone https://github.com/usadellab/gfftk.git
$: cd gfftk && mkdir build && cd $_ && ln -s ../config/Makefile
$: make gfftk

This should compile a gfftk executable in the directory build. This executable can be moved into any directory.

Examples

  • Assuming you are in gfftk/build
$: ./gfftk
$: ./gfftk extract -h
# Extract longest CDS and the corresponding prtotein_id attribute
$: ./gfftk extract -i GCF_000188115.4.ncbi.gff -t cds -l -a protein_id

Extract longest CDS from a GFF file and extract its corresponding sequence from the corresponding FASTA file (-f). Print to stdout:

$: ./gfftk extract -i GCF_000188115.4.ncbi.gff -t cds -l -f GCF_000188115.4.ncbi.fa