query genbank for an EST accession id

Description

extends the get.dna function of E Paradis CRAN package "ape"

Usage

get.dna2(access.nb)

Arguments

Details

queries ncbi

Value

a vector of nucleotide codes

Note

try ape::get.dna if this fails

Author(s)

VJ Carey <stvjc@channing.harvard.edu>

See Also

ape::get.dna

Examples

if (interactive())
{
data(IyerAnnotated)
get.dna2(IyerAnnotated$GB[1])
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Iyer517)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Iyer517/get.dna2.Rd_%03d_medium.png", width=480, height=480)
> ### Name: get.dna2
> ### Title: query genbank for an EST accession id
> ### Aliases: get.dna2
> ### Keywords: models
> 
> ### ** Examples
> 
> #if (interactive())
> #{
> data(IyerAnnotated)
> get.dna2(IyerAnnotated$GB[1])
Error in FI:LA : argument of length 0
Calls: get.dna2 -> unlist -> strsplit
Execution halted