apcamargo / parallel-prodigal

parallel-prodigal

./parallel-prodigal.py -i metagenome.fna -a proteins.faa -q -t 16

Modified from pprodigal. The changes include:

• Added support for compressed files (.gz, .bz2, and .xz).
• Automated chunk size determination.
• Fixed a bug where the contig IDs were not changed when concatenating the chuncks, causing repetition.
• Fixed a bug where \n was not added to the end of the lines when processing the outputs of the individual executions.
• Added a --quiet option that supresses output redirection to the standard output.
• Removed the "normal" mode. All Prodigal instances will use -p meta as self-training is unreliable when using chuncks of a larger assembly.