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.