p3-peg-kmer-hits

Count KMER Hits in Proteins

p3-peg-kmer-hits.pl [options] kmerDB

This script takes as input a list of genome IDs and outputs the best group for each protein feature in each genome. The output file will be tab-delimited, with the genomeID, the feature ID, the group ID, the group name, and the kmer hit count. The kmer database must specify protein kmers.

Parameters

The positional parameter is the file name of the kmer database. This is a json-format KmerDb object.

The standard input can be overridden using the options in Input Options.

Additional command-line options are those given in Column Options (to choose the genome ID column) plus the following options.

• verbose

If specified, progress messages will be written to STDERR.