p3-get-genome-sp-genes

Return Specialty Genes of the Specified Type in One or More Genomes

p3-get-genome-sp-genes.pl [options] property

This script returns specialty gene data for the genes in one of more genomes.

If you are searching based on genome_id then genome_id should be passed as standard input to CLI command as in example below

p3-all-genomes –eq genome_id,83332.12 –attr genome_id | p3-get-genome-sp-genes amr –attr patric_id,antibiotics,antibiotics_class,classification,gene,genome_id,feature_id,patric_id

The script recognizes the following types of specialty genes.

  • amr

Antibiotic Resistance

  • human

Human Homolog

  • target

Drug Target

  • transporter

Transporter

Parameters

The positional parameter is the type of specialty gene desired.

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

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

  • fields

List the available field names.

  • typeNames

List the available specialty gene types.

##TODO additional options