README.md

In felipepratalima/taxdumpr:

taxdumpr

prata Fri Sep 14 02:42:34 2018

knitr::opts_chunk$set(echo = TRUE)

taxdumpr is a R package which brings together a series of methods to manipulate NCBI's taxonomy data. It was developed to work locally, thorugh the NCBI's taxdump downloaded files. 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/taxdumpr") ## Instantiate the Taxdumpr base class

Load the package:

require(taxdumpr)

## Loading required package: 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. 3. mergedDmpLocation: the same to merged.dmp.

taxdumpr <- Taxdumpr(nodesDmpLocation = "~/taxdump/nodes.dmp", namesDmpLocation = "~/taxdump/names.dmp", mergedDmpLocation = "~/taxdump/merged.dmp")

Usage Examples

The getTaxonomyIdsByNames function should receive taxonomy name(s) and return taxonomy id(s):

getTaxonomyIdsByNames(taxdumpr, "Corynebacterium")

## [1] 1716

getTaxonomyIdsByNames(taxdumpr, "Corynebacterium variabile")

## [1] 1727

It works with synonyms too:

getTaxonomyIdsByNames(taxdumpr, "Caseobacter")

## [1] 1716

getTaxonomyIdsByNames(taxdumpr, "Caseobacter polymorphus")

## [1] 1727

The getUpdatedIds function should receive old taxonomy id(s) and new (updated) taxonomy id(s). In the example the ID 319938 is updated to the new ID 288004 (Beggiatoa leptomitoformis):

getUpdatedIds(taxdumpr, 319938)

## [1] 288004

Note that the non-updated ids are preserverd:

getUpdatedIds(taxdumpr, 288004)

## [1] 288004

getUpdatedIds(taxdumpr, c(319938, 1716, 1727, 288004))

## [1] 288004   1716   1727 288004

We recommend using getUpdatedIds always before starting to work with Taxdumpr.

The getScientificNamesByIds function should receive taxonomy id(s) and return the scientific name(s):

getScientificNamesByIds(taxdumpr, 1716)

## [1] "Corynebacterium"

getScientificNamesByIds(taxdumpr, 1727)

## [1] "Corynebacterium variabile"

The getScientificNamesByNames function should receive taxonomy name(s) and return the scientific name(s):

getScientificNamesByNames(taxdumpr, "Corynebacterium")

## [1] "Corynebacterium"

getScientificNamesByNames(taxdumpr, "Corynebacterium variabile")

## [1] "Corynebacterium variabile"

Synonyms:

getScientificNamesByNames(taxdumpr, "Caseobacter")

## [1] "Corynebacterium"

getScientificNamesByNames(taxdumpr, "Caseobacter polymorphus")

## [1] "Corynebacterium variabile"

The getTaxonomyRanksByIds function should receive taxonomy id(s) and return ranks(s):

getTaxonomyRanksByIds(taxdumpr, 1716)

## [1] "genus"

getTaxonomyRanksByIds(taxdumpr, 1727)

## [1] "species"

The getParentTaxonomyIdsByIds function should receive taxonomy id(s) and return parent id(s):

getParentTaxonomyIdsByIds(taxdumpr, 1716)

## [1] 1653

getParentTaxonomyIdsByIds(taxdumpr, 1727)

## [1] 1716

The getParentTaxonomyIdsByNames function should receive taxonomy name(s) and return parent taxonomy id(s):

getParentTaxonomyIdsByNames(taxdumpr, "Corynebacterium")

## [1] 1653

getParentTaxonomyIdsByNames(taxdumpr, "Corynebacterium variabile")

## [1] 1716

The getParentScientificNamesByIds function should receive taxonomy id(s) and return parent scientific name(s):

getParentScientificNamesByIds(taxdumpr, 1716)

## [1] "Corynebacteriaceae"

getParentScientificNamesByIds(taxdumpr, 1727)

## [1] "Corynebacterium"

The getParentScientificNamesByNames function should receive taxonomy name(s) and return parent scientific name(s):

getParentScientificNamesByNames(taxdumpr, "Corynebacterium")

## [1] "Corynebacteriaceae"

getParentScientificNamesByNames(taxdumpr, "Corynebacterium variabile")

## [1] "Corynebacterium"

The getStandardTaxonomyIdsByIds function should receive taxonomy id(s) of taxon(s) in non-standard level and return correspondent taxonomy id(s) in standard level:

## Non-standard
getStandardTaxonomyIdsByIds(taxdumpr, 290318)

## [1] 1094

getStandardTaxonomyIdsByIds(taxdumpr, 274493)

## [1] 191412

getStandardTaxonomyIdsByIds(taxdumpr, 1783270)

## [1] 2

## Standard
getStandardTaxonomyIdsByIds(taxdumpr, 1094)

## [1] 1094

The getStandardTaxonomyIdsByNames function should receive taxonomy name(s) in non-standard level and return correspondent taxonomy id(s) in standard level:

## Non-standard
getStandardTaxonomyIdsByNames(taxdumpr, "Chlorobium phaeovibrioides DSM 265")

## [1] 1094

getStandardTaxonomyIdsByNames(taxdumpr, "Chlorobium/Pelodictyon group")

## [1] 191412

getStandardTaxonomyIdsByNames(taxdumpr, "FCB group")

## [1] 2

## Standard
getStandardTaxonomyIdsByNames(taxdumpr, "Chlorobium phaeovibrioides")

## [1] 1094

The getStandardScientificNamesByNames function should receive taxonomy name(s) in non-standard level and return correspondent taxonomy name(s) in standard level:

## Non-standard
getStandardScientificNamesByNames(taxdumpr, "Chlorobium phaeovibrioides DSM 265")

## [1] "Chlorobium phaeovibrioides"

getStandardScientificNamesByNames(taxdumpr, "Chlorobium/Pelodictyon group")

## [1] "Chlorobiaceae"

getStandardScientificNamesByNames(taxdumpr, "FCB group")

## [1] "Bacteria"

## Standard
getStandardScientificNamesByNames(taxdumpr, "Chlorobium phaeovibrioides")

## [1] "Chlorobium phaeovibrioides"

The getLineageIdsByIds function should receive taxonomy id(s) and return complete taxonomy:

getLineageIdsByIds(taxdumpr, 290318)

##    taxonomyId lineageId
## 1      290318         2
## 2      290318   1783270
## 3      290318     68336
## 4      290318      1090
## 5      290318    191410
## 6      290318    191411
## 7      290318    191412
## 8      290318    274493
## 9      290318      1091
## 10     290318      1094
## 11     290318    290318

The getStandardLineageIdsByIds function should receive taxonomy id(s) and return standard taxonomy:

getStandardLineageIdsByIds(taxdumpr, 290318)

##    taxonomyId lineageId
## 1      290318         2
## 4      290318      1090
## 5      290318    191410
## 6      290318    191411
## 7      290318    191412
## 9      290318      1091
## 10     290318      1094

The getStandardLineageIdsByIdsAsDataFrame function should receive taxonomy id(s) and return standard taxonomy as DF = [taxonomyId, superkingdomId, phylumId, classId, orderId, familyId, genusId, speciesId]:

getStandardLineageIdsByIdsAsDataFrame(taxdumpr, 1094)

##   taxonomyId superkingdomId phylumId classId orderId familyId genusId
## 1       1094              2     1090  191410  191411   191412    1091
##   speciesId
## 1      1094

The getStandardLineageIdsAndScientificNamesByIdsAsDataFrame function should receive taxonomy id(s) and return standard taxonomy as DF = [taxonomyId, superkingdomId, phylumId, classId, orderId, familyId, genusId, speciesId, taxonomyName, superkingdomName, phylumName, className, orderName, familyName, genusName, speciesName]:

getStandardLineageIdsAndScientificNamesByIdsAsDataFrame(taxdumpr, 1094)

##   taxonomyId superkingdomId phylumId classId orderId familyId genusId
## 1       1094              2     1090  191410  191411   191412    1091
##   speciesId               taxonomyName superkingdomName phylumName
## 1      1094 Chlorobium phaeovibrioides         Bacteria   Chlorobi
##   className    orderName    familyName  genusName
## 1 Chlorobia Chlorobiales Chlorobiaceae Chlorobium
##                  speciesName
## 1 Chlorobium phaeovibrioides

felipepratalima/taxdumpr documentation built on May 14, 2019, 5:17 p.m.