--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/region_motif_intersect.r	Tue Aug 05 13:56:22 2014 -0400
@@ -0,0 +1,102 @@
+# Name: region_motif_intersect.r
+# Description: Takes a bed file of target regions and counts intersections
+# of each motif (built in rdata database) and target regions.
+# Author: Jeremy liu
+# Email: jeremy.liu@yale.edu
+# Date: 14/07/02
+# Note: This script is meant to be invoked with the following command
+# R --slave --vanilla -f ./region_motif_intersect.r --args <workingdir> <db> <inbed> <outtab>
+# <workingdir> is working directory of galaxy installation
+# <db> types: "t" test, "p" pouya, "j" jaspar jolma, "m" mouse
+# Dependencies: none
+
+# Auxiliary function to concatenate multiple strings
+concat <- function(...) {
+  input_list <- list(...)
+  return(paste(input_list, sep="", collapse=""))
+}
+
+# Set common and data directories
+args <- commandArgs()
+workingDir = args[7]
+commonDir = concat(workingDir, "/tools/my_tools")
+dbCode = args[8]
+if (dbCode == "t") {
+  motifDB = concat(commonDir, "/region_motif_db/pouya_test_motifs.bed.bgz")
+} else if (dbCode == "p") {
+  motifDB = concat(commonDir, "/region_motif_db/pouya_motifs.bed.bgz")
+} else if (dbCode == "j") {
+  motifDB = concat(commonDir, "/region_motif_db/jaspar_jolma_motifs.bed.bgz")
+} else if (dbCode == "m") {
+  motifDB = concat(commonDir, "/region_motif_db/mm9_motifs_split.bed.bgz")
+} else {
+  motifDB = concat(commonDir, "/region_motif_db/pouya_motifs.bed.bgz")
+}
+
+# Set input and reference files, comment to toggle commmand line arguments
+inBed = args[9]
+outTab = args[10]
+
+# Auxiliary function to read in BED file
+read_bed <- function(file) {
+  return(read.table(file, sep="\t", stringsAsFactors=FALSE))
+}
+
+startTime = Sys.time()
+cat("Running ... Started at:", format(startTime, "%a %b %d %X %Y"), "...\n")
+
+# Load dependencies
+#cat("Loading dependencies...\n")
+suppressPackageStartupMessages(library(Rsamtools, quietly=TRUE))
+
+# Initializing hash table (as env) with motif names and loading tabix file
+#cat("Loading motif database and initializing hash table...\n")
+motifTable = new.env()
+motifTbx <- TabixFile(motifDB)
+
+# Loading input bed file, convert integer columns to numeric, name columns
+#cat("Loading region file...\n")
+regionsDF = read_bed(inBed)
+dfTemp = sapply(regionsDF, is.integer)
+regionsDF[dfTemp] = lapply(regionsDF[dfTemp], as.numeric)
+names(regionsDF)[names(regionsDF) == "V1"] = "chr"
+names(regionsDF)[names(regionsDF) == "V2"] = "start"
+names(regionsDF)[names(regionsDF) == "V3"] = "end"
+
+# Filtering regions to exclude chromosomes not in motif database
+#cat("Determining intersection counts...\n")
+motifTbxChrs = seqnamesTabix(motifTbx)
+regionsDFFilter = subset(regionsDF, chr %in% motifTbxChrs)
+
+# Loading regions into GRanges object and scanning motif tabix database
+# Region end is incremented by 1 since scanTabix querying is inclusive for
+# position start but exclusive for position end.
+param = GRanges(regionsDFFilter$chr, IRanges(regionsDFFilter$start, 
+                end=regionsDFFilter$end + 1))
+regionsIntersects = scanTabix(motifTbx, param=param)
+
+# Parsing result list and updating motif count hash table
+#cat("Parsing result list...\n")
+for(regionIntersects in regionsIntersects) {
+  for(regionIntersect in strsplit(regionIntersects, " ")) {
+    intersectMotif = strsplit(regionIntersect, "\t")[[1]][4]
+    if(is.null(motifTable[[intersectMotif]])) {
+      motifTable[[intersectMotif]] = 1
+    } else {
+      motifTable[[intersectMotif]] = motifTable[[intersectMotif]] + 1
+    }
+  }
+}
+
+# Converting motif count hash table to an integer vector for output
+counts = integer(length = length(ls(motifTable)))
+names(counts) = ls(motifTable)
+for(motifName in ls(motifTable)) {
+  counts[motifName] = as.integer(motifTable[[motifName]])
+}
+
+# Outputting intersection counts to tab delineated file
+#cat("Outputting to file...\n")
+write.table(counts, outTab, quote=FALSE, sep="\t", row.names=TRUE, col.names=FALSE)
+cat("Done. Job started at:", format(startTime, "%a %b %d %X %Y."),
+    "Job ended at:", format(Sys.time(), "%a %b %d %X %Y."), "\n")