Py-pyrodigal

Python binding for Prodigal, an ORF finder for genomes and metagenomes

Pyrodigal is a Python module that provides bindings to Prodigal using Cython.

Features The library now features everything from the original Prodigal CLI

• run mode selection Choose between single mode, using a training sequence to count nucleotide hexamers, or metagenomic mode, using pre-trained data from different organisms prodigal -p.
• region masking Prevent genes from being predicted across regions containing unknown nucleotides prodigal -m.
• closed ends Genes will be identified as running over edges if they are larger than a certain size, but this can be disabled prodigal -c.
• training configuration During the training process, a custom translation table can be given prodigal -g, and the Shine-Dalgarno motif search can be forcefully bypassed prodigal -n
• output files Output files can be written in a format mostly compatible with the Prodigal binary, including the protein translations in FASTA format prodigal -a, the gene sequences in FASTA format prodigal -d, or the potential gene scores in tabular format prodigal -s.