added mdscore

Dockerfile

@@ -34,4 +34,8 @@ RUN make install
 # install R packages
 RUN R --vanilla -e 'install.packages(c("devtools", "BiocManager"), repos="http://cran.us.r-project.org")'
 RUN R --vanilla -e 'BiocManager::install(c("biomaRt", "copynumber", "GenVisR", "fgsea", "deseq2", "EBSeq", "BSgenome.Hsapiens.UCSC.hg19", "BSgenome.Hsapiens.UCSC.hg38", "TxDb.Hsapiens.UCSC.hg19.knownGene", "TxDb.Hsapiens.UCSC.hg38.knownGene", "org.Hs.eg.db", "NanoStringDiff"))'
-RUN R --vanilla -e 'install.packages(c("ggplot2", "data.table", "sequenza", "dplyr", "reshape2", "tidyr", "viridis", "cowplot", "ggalluvial", "msigdbr", "ggdendro", "gridExtra", "deconstructSigs", "tidyverse", "splitstackshape"), repos = "http://cran.us.r-project.org")'
+RUN R --vanilla -e 'install.packages(c("mdscore", "ggplot2", "data.table", "sequenza", "dplyr", "reshape2", "tidyr", "viridis", "cowplot", "ggalluvial", "msigdbr", "ggdendro", "gridExtra", "deconstructSigs", "tidyverse", "splitstackshape"), repos = "http://cran.us.r-project.org")'
+
+# copy any one-off R scripts over
+RUN mkdir -p /opt/scripts/R
+COPY scripts/optitype2imgt.R /opt/scripts/R

scripts/optitype2imgt.R

@@ -0,0 +1,45 @@
+################################################################################
+########### load in libraries and data #########################################
+
+# pass command line args
+args <- commandArgs(trailingOnly=TRUE)
+
+# hla predictions from optitype
+optitypeHLA <- read.delim(args[1])
+
+# imgt mapping between hla annotations and imgt ids
+alleleList <- read.csv(args[2], comment.char = "#")
+
+################################################################################
+############ convert HLA predictions to standard format ########################
+
+# grab just the HLA predictions
+keep <- c("A1", "A2", "B1", "B2", "C1", "C2")
+optitypeHLA <- as.character(t(optitypeHLA[,keep]))
+
+# make them consistent with IMGT allele list
+#optitypeHLA <- paste0("HLA-", optitypeHLA)
+
+################################################################################
+############ Grab the imgt HLA identifier for these ############################
+
+optitype2imgt <- function(x, y){
+  # find the imgt entries which corresond to the input
+  y <- y[grepl(x, y$Allele, fixed=TRUE),"AlleleID"]
+  y <- as.character(y[1])
+  return(y)
+}
+
+result <- unlist(lapply(optitypeHLA, optitype2imgt, alleleList))
+
+# make sure its unique
+result <- unique(result)
+
+################################################################################
+########### format and return the results ######################################
+
+# collapse and return
+result <- paste0(result, collapse=",")
+write(result, "")
+
+