p3-rep-prots

Create Representative Genome Server Directory

p3-rep-prots.pl [options] outDir

This script processes a list of genome IDs to create a directory suitable for use by the representative genomes server. It will extract all the instances of the specified seed protein (default is Phenylanyl synthetase alpha chain). The list of genome IDs and names will go in the output file complete.genomes and a FASTA of the seed proteins in 6.1.1.20.fasta.

Parameters

The positional parameter is the name of the output directory. If it does not exist, it will be created.

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

Additional command-line options are those given in Column Options plus the following options.

  • clear

Clear the output directory if it already exists. The default is to leave existing files in place.

  • prot

Role name of the protein to use. The default is Phenylalanyl-tRNA synthetase alpha chain.

  • dna

If specified, a 6.1.1.20.dna.fasta file will be produced in addition to the others, containing the DNA sequences of the proteins.

  • binning

If specified, a seed protein database suitable for binning will be produced with the specified name. (This is similar to the dna option, but produces the comments in a slightly different format).

  • debug

If specified, status messages for the PATRIC3 API will be displayed.