ORFget parameters#

Mandatory

-fna nucleotide fasta file of the genome whose ORFs are to extract

-gff gff annotation file

Optional

-h, --help shows this help message and exits

-features_include genomic features or annotation patterns to be searched for the ORF selection. ORFs whose annotations match the entered patterns or genomic features are written in the output fasta file. (default: all genomic features present in the input gff, consequently, all annotated ORFs will be written in the output gff file)(see the ORFget section for more details).

-features_exclude genomic features or annotation patterns to be searched for the ORF selection. ORFs whose annotations match the entered patterns or genomic features are not written in the output fasta file. (default: None, consequently, all annotated ORFs will be written in the output gff file)(see the ORFget section for more details).

-chr_exclude to exclude a (or a subset of) seqID(s) for the ORF extraction and writing - the ORFs belonging to this seqID (usually a chromosome or a contig) will not be written in the output fasta file no matter their annotation category (default: None).

-N number of ORFs randomly selected for the writing according to their genomic feature or pattern.