Usage

Exonize requires two positional arguments that can be followed by optional arguments. 

exonize <gff_file_path> <genome_file_path> [OPTIONS]

Required Arguments

  • <gff_file_path>: Path to the genome annotation file. This file should be in GFF3 or GFF format.
  • <genome_file_path>: Path to the genome sequence file. The file should be in FASTA format. A .zip version is also accepted.

Optional Arguments

  • [-gfeat]: Specifies the gene feature in the annotations file. Default: gene.
  • [-cdsfeat]: Specifies the coding sequence feature in the annotations file. Default: CDS.
  • [-transfeat]: Specifies the transcript feature in the genome annotations. Default: transcript.
  • [-sb]: Annotation coordinates base of input annotations, either 0 or 1. Default: 1.
  • [-fb]: Frame base of input annotations, either 0 or 1. Default: 0.
  • [-l]: Minimum exon length in bases required for the search. Default: 30.
  • [-e]: E-value threshold (local BLAST search param). Default: 1e-3.
  • [-ts]: Self-hit overlap threshold. Default: 0.5.
  • [-te]: Minimum query coverage cut-off. Default: 0.9.
  • [-ce]: Overlap threshold for constructing the set of representative exons. Default: 0.9.
  • [-ct]: Overlap threshold for target coordinate reconciliation (local BLAST search param). Default: 0.9.
  • [-tp]: Minimum length coverage between the query and target (global MUSCL search param). Default: 0.9.
  • [-ta]: Threshold for the fraction of aligned positions (global MUSCL search param). Default: 0.9.
  • [-ti]: Peptide identity threshold (global MUSCL search param). Default: 0.4.
  • [-op]: Search identifier. Default: The stem of the annotations file.
  • [-cn]: Number of CPUs to use. Default: The available CPU count.
  • [-odp]: Path to the output directory. Default: The current directory.
  • [--global-search]: Enables only the global search mode.
  • [--local-search]: Enables only the local search mode.
  • [--debug]: Enables debug mode, saving input and output files for the local search.
  • [--soft-force]: Overwrites the results database if it already exists.
  • [--hard-force]: Overwrites all internal files if they already exist.
  • [--csv]: Outputs a .zip file with a reduced set of results in CSV format.
  • [-v, --version]: Shows the program's version number and exits.
  • [-h, --help]: Shows this help message and exits.

NOTE: If neither flag --global-search or --local-search is specified, both searches will run by default.

Example: Human Y chromosome

The following steps demonstrate how to run exonize on a test dataset.

Download the test data

  • If you have installed the package from the repo, move into the test_human_chrom_Y directory and download the test data:
cd test_human_chrom_Y
source fetch_data.sh
  • If you installed the package via pip, you can download the script here: fetch_data.sh.

Run exonize with default parameters:

exonize Homo_sapiens.GRCh38.111.chromosome.Y.gff3 \
       Homo_sapiens.GRCh38.dna.chromosome.Y.fa.gz \
       --output_prefix Homo_sapiens_chrom_Y \
       --csv

This command will enable the global and local searches.