helixforge utils extract-proteins

Translate CDS from GFF3 + genome to protein FASTA.

Options

Option	Description
--gff3	Input GFF3. (required)
--genome	Reference genome FASTA. (required)
--out	Output protein FASTA. (required)
--longest-only, --all-isoforms	Keep only longest isoform per gene. (default: True)
--transl-table	NCBI translation table [default: 1]. (default: 1)
--min-length	Minimum protein length in aa [default: 30]. (default: 30)

Examples

  helixforge utils extract-proteins --gff3 genes.gff3 --genome genome.fa --out proteins.fa

  helixforge utils extract-proteins --gff3 genes.gff3 --genome genome.fa \
      --out proteins.fa --all-isoforms --min-length 50 --transl-table 11