inst/testScripts/complete/LambdaVirusExample/01a.downloadAnnotationData.R

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

path <- system.file("testScripts/R", package="aroma.seq");
pathname <- file.path(path, "downloadUtils.R");
source(pathname);

library("aroma.seq");
verbose <- Arguments$getVerbose(-8, timestamp=TRUE);

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Local functions
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
verbose && enter(verbose, "Downloading annotation data");

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Annotation data
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
path <- "annotationData/organisms/Lambda_phage/";
filename <- "lambda_virus.fa";
pathname <- Arguments$getReadablePathname(filename, path=path, mustExist=FALSE);

if (!isFile(pathname)) {
  downloadBowtie2ExampleData();
}

fa <- FastaReferenceFile(filename, path=path);
print(fa);

verbose && exit(verbose);