Merge 8c69c69 into be2d7d3

Dockerfile

@@ -1,10 +1,3 @@
-################################################################################
-##################### Add Container Labels #####################################
-LABEL "Regtools_License"="MIT"
-LABEL "Description"="Software package which integrate DNA-seq and RNA-seq data\
-                     to help interpret mutations in a regulatory and splicing\
-                     context."
-
 ################################################################################
 ##################### Set Inital Image to work from ############################
 
@@ -34,6 +27,13 @@ RUN apt-get update -y && apt-get install -y \
   cmake \
   python3
 
+################################################################################
+##################### Add Container Labels #####################################
+LABEL "Regtools_License"="MIT"
+LABEL "Description"="Software package which integrate DNA-seq and RNA-seq data\
+                     to help interpret mutations in a regulatory and splicing\
+                     context."
+
 ################################################################################
 ####################### Install R ##############################################
 
@@ -55,18 +55,18 @@ RUN R --vanilla -e 'install.packages(c("data.table", "plyr", "tidyverse"), repos
 ##################### Install Regtools #########################################
 
 # clone git repository
-RUN git clone https://github.com/griffithlab/regtools.git
+RUN cd / && git clone https://github.com/griffithlab/regtools.git
 
 # make a build directory for regtools
 WORKDIR /regtools/
-RUN mkdir build
+
 
 # compile from source
-RUN cd /regtools/build && cmake ..
-RUN cd /regtools/build && make
+RUN mkdir build && cd build && cmake .. && make
 
 ################################################################################
 ###################### set environment path    #################################
 
 # add regtools executable to path
-ENV PATH="/regtools/build:${PATH}"
+ENV PATH="/regtools/build:/usr/local/bin/R-${r_version}:${PATH}"
+

scripts/compare_junctions_hist_v2.R

@@ -9,21 +9,21 @@ library(tidyverse)
 
 debug = F
 
-system.time({
-if (debug){
-  tag = paste("_", "default", sep="")
-} else {
-  # get options tag
-  args = commandArgs(trailingOnly = TRUE)
-  tag = args[1]
-  input_file = args[2]
-  if ( substr(tag, 2, 3) == "--"){
-    stop("Please specify an option tag (e.g. \"default\", \"i20e5\")")
-  }
-}
+# system.time({
+# if (debug){
+#   tag = paste("_", "default", sep="")
+# } else {
+#   # get options tag
+#   args = commandArgs(trailingOnly = TRUE)
+#   tag = args[1]
+#   input_file = args[2]
+#   if ( substr(tag, 2, 3) == "--"){
+#     stop("Please specify an option tag (e.g. \"default\", \"i20e5\")")
+#   }
+# }
 
-# tag = 'I'
-# input_file = '~/Desktop/CHOL/all_splicing_variants_I.bed'
+tag = 'E'
+input_file = 'all_splicing_variants_E.bed'
 
 # All splicing relevant variants (union of rows from variants.bed files; add column with comma-separated list of sample names)
 all_splicing_variants = unique(data.table::fread(input_file), sep = '\t', header = T, stringsAsFactors = FALSE)
@@ -150,21 +150,14 @@ regtools_data = subset(regtools_data, select=columns_to_keep)
 
 
 # zeroes need to be added in for some samples
-a <- function(x, y, z){
+a <- function(x, y){
   toAdd <- y - length(x) - 1
   # browser()
   toAdd <- rep(0.0000000, toAdd)
   x <- c(x, toAdd)
   return(x)
 }
-x <- mapply(a, regtools_data$norm_scores_non, length(all_samples), regtools_data$samples)
-
-
-# if (typeof(x) == 'list') {
-#   x <- matrix(pad(unlist(x), ncols),nrow = rows, byrow = TRUE, ncol = cols)
-#   x <- t(x)
-#   }
-# browser()
+x <- mapply(a, regtools_data$norm_scores_non, length(all_samples))
 
 get_num_zeros_to_rm <- function(z){
   num_zeroes_to_rm = str_count(z, ',') 
@@ -188,6 +181,47 @@ if (max(num_zeroes_to_rm > 0)) {
 x <- mapply(rm_zeroes, regtools_data$norm_scores_non, regtools_data$zeroes_to_rm)
 regtools_data$norm_scores_non = x
 }
+
+get_mean <- function(x){
+  x <- mean(as.numeric(x))
+  return(x)
+}
+
+x <- mapply(get_mean, regtools_data$norm_scores_non) 
+regtools_data$mean_norm_score_non <- x
+
+get_sd <- function(x){
+  x <- sd(as.numeric(x))
+  return(x)
+}
+
+x <- mapply(get_sd, regtools_data$norm_scores_non) 
+regtools_data$sd_norm_score_non <- x
+
+a <- function(x, y){
+  # if(y == "TCGA-ZH-A8Y2-01A,TCGA-ZH-A8Y5-01A"){
+  #    browser()
+  # }
+  toAdd <- (str_count(y, ',') + 1) - (str_count(x, ',') + 1) 
+  # browser()
+  if (toAdd > 0) {
+    toAdd <- rep(0.0000000, toAdd)
+    x <- c(x, toAdd)
+  } else {
+    x <- unlist(strsplit(x, ","))
+  }
+  x <- list(x)
+  return(x)
+}
+x <- mapply(a, regtools_data$norm_scores_variant, regtools_data$samples)
+regtools_data$norm_scores_variant = x
+
+x <- mapply(get_mean, regtools_data$norm_scores_variant) 
+regtools_data$mean_norm_score_variant <- x
+
+x <- mapply(get_sd, regtools_data$norm_scores_variant) 
+regtools_data$sd_norm_score_variant <- x
+
 print("test7")
 
 ################ calculate p-values ############################################
@@ -207,9 +241,6 @@ a <- function(x){
                   breaks = seq(0.5, max(non_variant_norm_scores_ranked)+1.5, by=1), plot=F)
   mids = histinfo$mids
   cd = cumsum(histinfo$density)
-  # if(x$info == "chr1_729955_735423_D_chr1:809966-809967"){
-  #   browser()
-  # }
   underestimate = max(which(mids <= variant_norm_score_ranked))
   pvalue = 1-cd[underestimate]
   return(pvalue)
@@ -243,5 +274,5 @@ regtools_data = regtools_data %>% distinct()
 
 
 write.table(regtools_data, file=paste(input_file, "_out.tsv", sep=""), quote=FALSE, sep='\t', row.names = F)
-
-})
+# 
+# })