carnivoreSeqRuns: Download sequencing run files for a carnivore biome dataset

In derele/MultiAmplicon: Metabarcoding and microbiome analysis using multiple amplicons

Download sequencing run files for a carnivore biome dataset

Description

For use in the [real-world data vignette](https://derele.github.io/MultiAmplicon/articles/MultiAmplicon-real-world-example.html)), we download a dataset containing details of the SRA dataset for BioProject PRJNA386767 "Intestinal biome sequencing of carnivores". We download the sample data from SRA, re-format it for our later analysis. And use the SRA run ids to download the raw sequencing files for precessing in the vignette.

Usage

carnivoreSeqRuns

Format

An object of class data.frame with 192 rows and 5 columns.

Source

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA386767

Examples

## This data was generated in R using the following code:
## Not run: 
## create an SRA database connection
library(SRAdb)
sqlfile <- "SRAmetadb.sqlite"
if(!file.exists(sqlfile)){
    sqlfile <- getSRAdbFile()
}

sra_con <- dbConnect(SQLite(),sqlfile)

carnivoreSeqRuns <- getSRA(search_terms = '"Intestinal biome sequencing of carnivores"',
                           sra_con=sra_con, acc_only=FALSE)

carnivoreSeqRuns <- carnivoreSeqRuns[, c('run','study','sample',
                                       'experiment', 'sample_attribute')]

sample.vars <- strsplit(carnivoreSeqRuns$sample_attribute, " \\|\\| ")

sample.variable <- lapply(sample.vars, function(x){
    what <- strsplit(x, ": ")
    variable <- lapply(what, "[[", 2)
    names(variable) <- lapply(what, "[[", 1)
    variable
})

carnivoreSeqRuns <- cbind(carnivoreSeqRuns, do.call(rbind, sample.variable))

carnivoreSeqRuns$sample_attribute <- NULL

runs <- carnivoreSeqRuns$run

destDir <- "download_sra"

if(!file_test("-d", destDir)) dir.create(destDir)

fastqFiles <- list.files(destDir, pattern=".fastq.gz", full.names=TRUE)

if(!length(fastqFiles)){
    getSRAfile(runs, sra_con, fileType = 'fastq' , srcType = "ftp",
               destDir=destDir)
    fastqFiles <- list.files(destDir, pattern=".fastq.gz", full.names=TRUE)
  }

## End(Not run)

derele/MultiAmplicon documentation built on Oct. 14, 2023, 7:43 p.m.