summary.py

usage: summary.py

Summarize Autometa results writing genome fastas and their respective
taxonomies/assembly metrics for respective metagenomes

optional arguments:
  -h, --help            show this help message and exit
  --binning-main filepath
                        Path to Autometa binning main table (output from
                        --binning-main argument) (default: None)
  --markers filepath    Path to annotated markers respective to domain
                        (bacteria or archaea) binned (default: None)
  --metagenome filepath
                        Path to metagenome assembly (default: None)
  --dbdir dirpath       Path to user taxonomy database directory (Required for
                        retrieving metabin taxonomies) (default: None)
  --dbtype {ncbi,gtdb}  Taxonomy database type to use (NOTE: must correspond
                        to the same database type used during contig taxon
                        assignment.) (default: ncbi)
  --binning-column str  Binning column to use for grouping metabins (default:
                        cluster)
  --output-stats filepath
                        Path to write metabins stats table (default: None)
  --output-taxonomy filepath
                        Path to write metabins taxonomies table (default:
                        None)
  --output-metabins dirpath
                        Path to output directory. (Directory must not exist.
                        This directory will be created.) (default: None)