p3-get-family-features

Return Features From Families in PATRIC

p3-get-family-features [options]

This script returns data for all the features in one or more protein families from the PATRIC database. It supports standard filtering parameters and the specification of additional columns if desired. In addition, the results can be filtered by genomes from a secondary input file. As currently coded, the command may fail if the number of genomes in the secondary file is large.

Parameters

There are no positional parameters.

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.

gFile

Name of a tab-delimited file containing genome IDs. If specified, only features in these genomes will be returned.

gCol

Index (1-based) or header name of the column containing the genome IDs in the genome file. The default is genome.genome_id.

ftype

The type of family being used. The default is local, indicating PATRIC local protein families. Other options are figfam or global.

fields

List the available field names.