p3-get-genome-refseq-features

Return Features From Genomes in BV-BRC

p3-get-genome-refseq-features [options]

This script returns data for all the non-BV-BRC (RefSeq) features in one or more genomes from the BV-BRC database. It supports standard filtering parameters and the specification of additional columns if desired.

Parameters

There are no positional parameters.

The standard input can be overriddn 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 fields.

• selective

If specified, the number of features per genome is expected to be small, so a faster algorithm can be used.

Example

This command is shown in the tutorial p3_CLI.html

p3-all-genomes --eq genus,Methylobacillus | p3-get-genome-features --attr patric_id --attr product
genome.genome_id        feature.patric_id       feature.product
265072.11       fig|265072.11.rna.17    tRNA-Arg-CCG
265072.11       fig|265072.11.rna.18    tRNA-Lys-TTT
265072.11       fig|265072.11.rna.19    tRNA-Arg-ACG
265072.11       fig|265072.11.rna.20    tRNA-Ser-GCT
265072.11       fig|265072.11.rna.37    tRNA-Gly-GCC
...