extractCarboGenes: Extract Simple Sugar Degradation Genes from A Microbial...

In MolyWang/microCompet: Identify A Microbe's Potential Nutrition Competitor From Microbiota

Extract Simple Sugar Degradation Genes from A Microbial Genome

Description

This function reads a user-provided genbank file line by line and extracts genes encoding enzymes that participate in simple sugar degradation as a vector.

Usage

extractCarboGenes(genomeFilePath, fullEnzymeGeneVec)

Arguments

genomeFilePath	Full path to a GenBank file that represents a microbial genome. This GenBank file must at least have gene names annotated. See provided file "Klebsiella_variicola.gb" and "Lactobacillus_johnsonii.gb" in extdata for example, they have lines in the format /gene="geneName". And see example for how to extract full path to the example files. (genomeFilePath <- part)
fullEnzymeGeneVec	A list of all sugar degradation genes to be searched for in the user-provided genome (the file with genomeFilePath).

Details

There are other available packages that format the whole genbank file into one organized object, but information other than geneName are not useful to this package, and those functions would take about 30 more seconds on a Windows system, so this function is provided.

Value

A vector of gene names that encode simple sugar degradation enzymes.

Examples

## Not run: 
 require("microCompet")
 ED <- microCompet::EnzymeDistribution
 fullEnzymeGeneVec <- ED$Gene
 genomeFilePath <- system.file("extdata",
                               "Klebsiella_variicola.gb",
                               package = "microCompet",
                               mustWork = TRUE)
 carboGenes <- extractCarboGenes(genomeFilePath, fullEnzymeGeneVec)
 carboGenes

## End(Not run)

MolyWang/microCompet documentation built on Feb. 26, 2023, 9:29 p.m.