Commit 2a476c9f authored by VladaMilch's avatar VladaMilch
Browse files

small bugs fixed

parent c686de4e
......@@ -10,7 +10,7 @@
#' @param min_probe_number numeric, minimal number or probes in a probe set
#' @param pkgNameSUFFIX character, suffix to the package name, usually starts with dor: '.hereIsYourSuffix'
#' @param quiet logical
#' @param fastaDir directory used for generation of the FASTA files
#' @param packageOutDir directory where a new package will be written (note: SQL works poorly on a cluster, and one might want to write a package somewhere else)
#' @return a \code{"output type"}.
#' @seealso \code{function or class name}
#' @author Vladislava Milchevskaya \email{milchv@gmail.com}
......@@ -41,12 +41,12 @@ makeNewAnnotationPackage <- function(alignment.dir,
min_probe_number,
quiet=FALSE,
pkgNameSUFFIX,
fastaDir)
packageOutDir)
{
if(!file.exists( file.path(fastaDir, "tmpProbesTableDir/seed3.RData")))
{stop("Please provide the directory used to generate fasta files in the previous step (fastaDir). \n")}
if(!file.exists( file.path(outputDir, "tmpProbesTableDir/seed3.RData")))
{stop("Please provide the directory used to generate fasta files in the previous step (outputDir). \n")}
load(file.path(fastaDir, "tmpProbesTableDir/seed3.RData"))
load(file.path(outputDir, "tmpProbesTableDir/seed3.RData"))
new_pd <- makeNewAnnotationPackage_inner(alignment.dir = alignment.dir,
Annotation = Annotation,
package_seed = seed3,
......@@ -55,7 +55,7 @@ makeNewAnnotationPackage <- function(alignment.dir,
min_probe_number = min_probe_number,
quiet=quiet,
pkgNameSUFFIX = pkgNameSUFFIX,
fastaDir=fastaDir)
packageOutDir=packageOutDir)
# debugging msg start
cat(paste0(names(new_pd)))
# debugging msg end
......@@ -73,7 +73,7 @@ makeNewAnnotationPackage_inner <- function(alignment.dir,
min_probe_number,
quiet=FALSE,
pkgNameSUFFIX,
fastaDir=fastaDir
packageOutDir=packageOutDir
)
{
stopifnot(class(pkgNameSUFFIX) == "character")
......@@ -82,14 +82,14 @@ makeNewAnnotationPackage_inner <- function(alignment.dir,
# checks for input parameters for alignments2parsedData inside the function
NEW_ParsedData <- alignments2parsedData(alignment.dir = alignment.dir,
Annotation = Annotation,
outputDir = fastaDir,
outputDir = outputDir,
level = level,
min_probe_number = min_probe_number,
package_seed = package_seed)
make_package_from_parsedData(parsedData = NEW_ParsedData,
object = package_seed[[1]], #seed
destDir = fastaDir,
destDir = packageOutDir,
quiet = quiet,
pkgNameSUFFIX = pkgNameSUFFIX,
annotation_type = package_seed[[3]])
......
......@@ -5,7 +5,7 @@
\title{What function does (short)}
\usage{
makeNewAnnotationPackage(alignment.dir, Annotation, outputDir, level,
min_probe_number, quiet = FALSE, pkgNameSUFFIX, fastaDir)
min_probe_number, quiet = FALSE, pkgNameSUFFIX, packageOutDir)
}
\arguments{
\item{alignment.dir}{path to the directory that contains alignment files}
......@@ -21,6 +21,8 @@ makeNewAnnotationPackage(alignment.dir, Annotation, outputDir, level,
\item{quiet}{logical}
\item{pkgNameSUFFIX}{character, suffix to the package name, usually starts with dor: '.hereIsYourSuffix'}
\item{packageOutDir}{directory where a new package will be written (note: SQL works poorly on a cluster, and one might want to write a package somewhere else)}
}
\value{
a \code{"output type"}.
......
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