py311-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).