NLR_myrtacae
###NLR_filter_gene_models.py
Prerequiste:
- Bedtools and pybedtools
- pandas
- Biopython
- getAnnoFasta.pl from Augustus in the PATH
- python 3.5+
- assume to be run in the folder that also contains the original PREFIX.fa genome file used for NLR annotator
usage: NLR_filter_gene_models.py [-h] anno_fn [anno_fn ...] pfam_fn [pfam_fn ...] fa_fn [fa_fn ...] pro_fn [pro_fn ...]
This program parses out the gene models on the identified NLR loci. It filters them for NB-ARC domain containing proteins only. Works with augustus.gff3 or braker.gtf. It needs 'gene' in the feature column. It needs 'transcript_id' and 'gene_id' in the featur column.
positional arguments: anno_fn Please provide a gtf or gff3 annotation file. pfam_fn Please provide pfam output file for the corresponding proteins. fa_fn Please provide NLR loci filename used for gene prediction. pro_fn Please provide protein filename of the annotated gene models.
optional arguments: -h, --help show this help message and exit