p3-submit-codon-tree

Submit a Phylogenetic Tree Mapping Request

This script submits a request to build a codon tree to BV-BRC. This is a slow process and the job can take more than one day, depending on the number of genoems. It takes a list of BV-BRC genome IDs as input and accepts a few additional parameters.

Usage Synopsis

p3-submit-codon-tree [options] output-path output-name

Start a phylogenetic tree mapping job, producing output in the specified workspace path, using the specified name for the base filename of the output files.

Command-Line Options

  • –workspace-path-prefix

Prefix to be put in front of the output path. This is optional, and is provided for uniformity with other commands.

  • –genome-ids

Main list of genome IDs, comma-delimited. Alternatively, this can be a local file name. If specified, the file must be tab-delimited, with a header line, containing the genome IDs in the first column. The genome IDs in this file can optionally be enclosed in quotes, allowing a text file download of a BV-BRC genome group or genome display to be used.

  • –number-of-genes

Number of marker genes to use for building the tree (default 100).

  • –max-genomes-missing

The maximum number of genomes that can be missing from any PGFam before the family is disqualified.

  • –max-allowed-dups

The maximum number of genoems that can have multiple proteins from a PGFam before the family is disqualified.

  • –help

Display the command-line usage and exit.

  • –dry-run

Display the JSON submission string and exit without invoking the service or uploading files.