p3-gto-fasta

Convert Genome Typed Objects to FASTA

p3-gto-fasta.pl [options] gtoFile

This script produces FASTA files from a GenomeTypeObject instance. The GTO must be provided as a file in JSON format.

Parameters

The positional parameter is the name of the GTO file. If none is specified, the GTO file is read from the standard input.

The command-line options are the following. All three are mutually exclusive.

• protein

If specified, the output will be a protein FASTA file.

• feature

If specified, the output will be a feature DNA FASTA file.

• contig

If specified, the output will be a contig DNA FASTA file. this is the default.