Nothing
############################################################################
# Author: Henrik Bengtsson
# Created on: 2010-05-26
# Last updated: 2010-05-26
#
# USAGE:
# path <- "downloadScripts/chipTypes/Mapping50K_Hind240,Xba240";
# filename <- "HapMap,testSet,100K.R";
# pathname <- system.file(path, filename, package="aroma.affymetrix");
# source(pathname);
#
# DOWNLOADS:
# rawData/
# HapMap,testSet/
# Mapping50K_Hind240/
# CEU_NA06985_HIND.CEL, CEU_NA06991_HIND.CEL, CEU_NA06993_HIND.CEL,
# CEU_NA06994_HIND.CEL, CEU_NA07000_HIND.CEL, CEU_NA07019_HIND.CEL
# Mapping50K_Xba240/
# CEU_NA06985_XBA.CEL, CEU_NA06991_XBA.CEL, CEU_NA06993_XBA.CEL,
# CEU_NA06994_XBA.CEL, CEU_NA07000_XBA.CEL, CEU_NA07019_XBA.CEL
############################################################################
library("R.filesets");
verbose <- Arguments$getVerbose(-5, timestamp=TRUE);
urlPath <- "ftp://ftp.ncbi.nlm.nih.gov/hapmap/raw_data/affy100k/";
files <- list(
"Mapping50K_Hind240" = c(
"CEU_NA06985_HIND.CEL.gz",
"CEU_NA06991_HIND.CEL.gz",
"CEU_NA06993_HIND.CEL.gz",
"CEU_NA06994_HIND.CEL.gz",
"CEU_NA07000_HIND.CEL.gz",
"CEU_NA07019_HIND.CEL.gz"
),
"Mapping50K_Xba240" = c(
"CEU_NA06985_XBA.CEL.gz",
"CEU_NA06991_XBA.CEL.gz",
"CEU_NA06993_XBA.CEL.gz",
"CEU_NA06994_XBA.CEL.gz",
"CEU_NA07000_XBA.CEL.gz",
"CEU_NA07019_XBA.CEL.gz"
)
);
rootPath <- "rawData";
dataSet <- "HapMap,testSet";
chipTypes <- names(files);
dsList <- list();
for (kk in seq_along(chipTypes)) {
chipType <- chipTypes[kk];
verbose && enter(verbose, sprintf("Chip type #%d ('%s') of %d",
kk, chipType, length(chipTypes)));
path <- file.path(rootPath, dataSet, chipType);
filenames <- files[[chipType]];
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Download only files if missing (with or without *.gz)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
pathnames <- file.path(path, filenames);
pathnames <- sapply(pathnames, FUN=filePath, expandLinks="any");
# Gunzip already downloaded *.gz files
keep <- sapply(pathnames, FUN=isFile);
ds <- GenericDataFileSet(lapply(pathnames[keep], FUN=GenericDataFile));
sapply(ds, gunzip, verbose=TRUE);
# See what is missing
pathnames <- gsub(".gz", "", pathnames, fixed=TRUE);
keep <- !sapply(pathnames, FUN=isFile);
filenames <- filenames[keep];
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Download and gunzip
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (length(filenames) > 0) {
# Download
urls <- paste(urlPath, filenames, sep="");
pathnamesZ <- sapply(urls, FUN=downloadFile, path=path, verbose=TRUE);
verbose && print(verbose, pathnamesZ);
# Gunzip the data files
ds <- GenericDataFileSet(lapply(pathnamesZ, FUN=GenericDataFile));
sapply(ds, gunzip, verbose=TRUE);
verbose && cat(verbose, "Downloaded:");
verbose && print(verbose, ds);
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ds <- GenericDataFileSet(lapply(pathnames, FUN=GenericDataFile));
verbose && cat(verbose, "Complete file set:");
verbose && print(verbose, ds);
dsList[[chipType]] <- ds;
verbose && exit(verbose);
} # for (chipType ...)
verbose && print(verbose, dsList);
############################################################################
# HISTORY:
# 2010-05-26
# o Created.
############################################################################
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