P3 Command Line Interface

[brettin]

The p3-all-genomes has limited usage without knowing the field names. Here is an example of a solution to help illustrate how I work.

brettin@golgi:~$ p3-get_genomes --show-fields
version
assembly_accession
assembly_method
bioproject_accession
biosample_accession
class
collection_date
comments
common_name
completion_date
contigs
date_inserted
date_modified
document_type
family
gc_content
genbank_accessions
genome_id
genome_length
genome_name
genome_status
genus
geographic_location
host_name
isolation_country
isolation_source
kingdom
order
owner
patric_cds
phylum
public
publication
refseq_accessions
refseq_cds
sequences
sequencing_centers
sequencing_depth
sequencing_platform
species
strain
taxon_id
taxon_lineage_ids
taxon_lineage_names