API Reference

This section contains a complete reference of the pyrodigal module API.

Gene Finder

pyrodigal.GeneFinder

A configurable gene finder for genomes and metagenomes.

Training Info

pyrodigal.TrainingInfo

A collection of parameters obtained after training.

Metagenomic Bin

pyrodigal.MetagenomicBin	A pre-trained collection used to find genes in metagenomic mode.
pyrodigal.MetagenomicBins	An indexed list of MetagenomicBin to use in meta-mode.

Genes

pyrodigal.Genes	A list of raw genes found by Prodigal in a single sequence.
pyrodigal.Gene	A single raw gene found by Prodigal within a DNA sequence.

Nodes

pyrodigal.Nodes	A list of dynamic programming nodes used by Prodigal to score ORFs.
pyrodigal.Node	A dynamic programming node used by Prodigal to score ORFs.

Sequence

pyrodigal.Sequence

A digitized input sequence.

Masks

pyrodigal.Masks	A list of masked regions within a Sequence.
pyrodigal.Mask	The coordinates of a masked region.