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.