p3-all-genomes¶

Return All Genomes in BV-BRC¶

p3-all-genomes [options]

This script returns the IDs of all the genomes in the BV-BRC database. It supports standard filtering parameters and the specification of additional columns if desired.

Parameters¶

There are no positional parameters.

The command-line options are those given in Data Options plus the following.

fields

List the names of the available fields.

public

Only include public genomes. If this option is NOT specified and you are logged in (via p3-login), your own private genomes will also be included in the output.

private

Only include private genomes. If this option is specified and you are not logged in, there will be no output. It is mutually exclusive with public.

You can peruse

https://github.com/PATRIC3/patric_solr/blob/master/genome/conf/schema.xml

to gain access to all of the supported fields. There are quite a

few, so do not panic. You can use something like

p3-all-genomes -a genome_name -a genome_length -a contigs -a genome_status

to get some commonly sought fields.

Example¶

This command is used in several tutorials, see p3_CLI.html for example;

p3-all-genomes --eq genome_name,Streptomyces --attr genome_id --attr genome_name

This example retrieves the id and genome name for all genomes having Streptomyces in their name.

genome.genome_id    genome.genome_name
284037.4    Streptomyces sporocinereus strain OsiSh-2
67257.17    Streptomyces albus subsp. albus strain NRRL F-4371
68042.5 Streptomyces hygroscopicus subsp. hygroscopicus strain NBRC 16556
68042.6 Streptomyces hygroscopicus subsp. hygroscopicus strain NBRC 13472
1395572.3   Streptomyces albulus PD-1
...