changeset 13:00627aa25b6c draft

Update relative directories within intersect.r

--- a/region_motif_intersect.r	Fri Nov 07 12:37:44 2014 -0500
+++ b/region_motif_intersect.r	Fri Nov 07 12:38:18 2014 -0500
@@ -19,18 +19,18 @@
 # Set common and data directories
 args <- commandArgs()
 workingDir = args[7]
-commonDir = concat(workingDir, "/tools/my_tools")
+dbDir = concat(workingDir, "/region_motif_db")
 dbCode = args[8]
 if (dbCode == "t") {
-  motifDB = concat(commonDir, "/region_motif_db/pouya_test_motifs.bed.bgz")
+  motifDB = concat(dbDir, "/pouya_test_motifs.bed.bgz")
 } else if (dbCode == "p") {
-  motifDB = concat(commonDir, "/region_motif_db/pouya_motifs.bed.bgz")
+  motifDB = concat(dbDir, "/pouya_motifs.bed.bgz")
 } else if (dbCode == "j") {
-  motifDB = concat(commonDir, "/region_motif_db/jaspar_jolma_motifs.bed.bgz")
+  motifDB = concat(dbDir, "/jaspar_jolma_motifs.bed.bgz")
 } else if (dbCode == "m") {
-  motifDB = concat(commonDir, "/region_motif_db/mm9_motifs_split.bed.bgz")
+  motifDB = concat(dbDir, "/mm9_motifs.bed.bgz")
 } else {
-  motifDB = concat(commonDir, "/region_motif_db/pouya_motifs.bed.bgz")
+  motifDB = concat(dbDir, "/pouya_motifs.bed.bgz")
 }
 
 # Set input and reference files, comment to toggle commmand line arguments
@@ -46,16 +46,16 @@
 cat("Running ... Started at:", format(startTime, "%a %b %d %X %Y"), "...\n")
 
 # Load dependencies
-#cat("Loading dependencies...\n")
+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")
+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")
+cat("Loading region file...\n")
 regionsDF = read_bed(inBed)
 dfTemp = sapply(regionsDF, is.integer)
 regionsDF[dfTemp] = lapply(regionsDF[dfTemp], as.numeric)
@@ -64,7 +64,7 @@
 names(regionsDF)[names(regionsDF) == "V3"] = "end"
 
 # Filtering regions to exclude chromosomes not in motif database
-#cat("Determining intersection counts...\n")
+cat("Determining intersection counts...\n")
 motifTbxChrs = seqnamesTabix(motifTbx)
 regionsDFFilter = subset(regionsDF, chr %in% motifTbxChrs)
 
@@ -76,7 +76,7 @@
 regionsIntersects = scanTabix(motifTbx, param=param)
 
 # Parsing result list and updating motif count hash table
-#cat("Parsing result list...\n")
+cat("Parsing result list...\n")
 for(regionIntersects in regionsIntersects) {
   for(regionIntersect in strsplit(regionIntersects, " ")) {
     intersectMotif = strsplit(regionIntersect, "\t")[[1]][4]
@@ -96,7 +96,7 @@
 }
 
 # Outputting intersection counts to tab delineated file
-#cat("Outputting to file...\n")
+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")