README.md

In felipepratalima/gunga:

gunga

prata Fri Aug 17 17:08:15 2018

knitr::opts_chunk$set(echo = TRUE)

gunga is a R package which ... . It was developed using the S4 class system, by Felipe Prata Lima (http://lbi.usp.br/membros/) and João Carlos Setubal (http://www.iq.usp.br/setubal/).

taxdump files download

The taxdump files can be download from the NCBI's ftp site, at ftp://ftp.ncbi.nih.gov/pub/taxonomy/. You can download these files using wget with the command:

wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

And uncompress it using tar:

tar zxvf taxdump.tar.gz

This way you should obtain the following files:

ls ~/taxdump/

## citations.dmp
## delnodes.dmp
## division.dmp
## gc.prt
## gencode.dmp
## merged.dmp
## names.dmp
## nodes.dmp
## readme.txt
## taxdump.tar.gz

In this docs, we are going to suppose that you downloaded and uncompressed this in your home folder. ## Install

Install the package using devtools:

devtools::install_github("felipepratalima/gunga") ## Instantiate the Taxdumpr base class

Load the package:

# require(taxdumpr)

Packages methods are organized around the Taxdumpr object. This can be instatiated by the Taxdumpr constructor, which requires: 1. nodesDmpLocation: the path to the nodes.dmp file from taxdump downloaded files. 2. namesDmpLocation: the same to names.dmp.

# taxdumprObject <- Taxdumpr(nodesDmpLocation = "~/taxdump/nodes.dmp", namesDmpLocation = "~/taxdump/names.dmp")

Usage Examples

Centrifuge (Shotgun) + Spingo + QIIME

felipepratalima/gunga documentation built on Aug. 16, 2019, 10:14 p.m.