hkgfinder 0.2.0

find housekeeping genes in prokaryotic (meta)genomic data

hkgfinder

Find housekeeping genes in prokaryotic (meta)genomes

Introduction

hkgfinder is a fast and accurate housekeeping gene finder and classifier. hkgfinder can run on raw sequences, genomes and metagenomes. The novel value of this method lies is in its ability to directly predict and classify gene sequences into housekeeping gene families at a high specificity and sensitivity, while being also faster than genome and metagenome annotator on genome and metagenome data.

How hkgfinder works

Installation

You will have first to install Prodigal and HMMER 3 to be able to run hkgfinder.

hkgfinder since v0.2 is without external dependencies.

pip install hkgfinder

Test

• Type hkgfinder -h and it should output something like:

usage: hkgfinder [options] [<FILE>]

options:
  -o [FILE]      output result to FILE [stdout]
  -g             activate genome mode [false]
  -m             activate metagenome mode [false]
  --faa FILE     output matched protein sequences to FILE [false]
  --fna FILE     output matched DNA sequences to FILE [false]
  -s             output sequences in file by gene [false]
  -t INT         number of threads [1]
  -q             decrease program verbosity
  -d             enable debug mode
  -v, --version  show program's version number and exit
  -h, --help     show this help message and exit

Invoking hkgfinder

hkgfinder --faa housekeeping.faa --fna housekeeping.fna file.fa.gz

• hkgfinder supports gzip, lzma, bz2 and zstd compressed files.

Bugs

Submit problems or requests to the Issue Tracker.

Licence

MIT.

Author

• Anicet Ebou