p3-role-fasta

Create Fasta File for a Role

p3-role-fasta.pl [options] roleDesc

This script takes as input a list of genome IDs and outputs a FASTA file containing the features in those genomes possessing a specified role.

Parameters

The positional parameter is the name of the role to use.

The standard input can be overridden using the options in Input Options. It should contain a genome ID in the key column identified by the Column Options.

Additional command-line options are as follows.

  • binning

The output file is for a binning database. The comment will be a genome ID and the name. Implies both --dna and --nodups.

  • dna

If specified, the output will be DNA sequences. The default is protein sequences.

  • verbose

Progress messages will be displayed on STDERR.

  • noDups

If specified, roles that occur multiple times in the same genome will be discarded.