diff get_fm_at_midpoint.R @ 0:6d6dc275b107 draft

planemo upload commit 0fca33c3b7285bd31f6c7380393d08bbdad4e4d6

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_fm_at_midpoint.R	Mon Aug 15 23:48:20 2016 -0400
@@ -0,0 +1,60 @@
+
+library(wrassp)
+
+get_fm_at_midpoint <- function(segments, wavmap) {
+    midpoint_fm <- function(row) {
+        start = as.numeric(row[1])
+        end = as.numeric(row[2])
+        identifier = row[5]
+        fn = wavmap[identifier]
+        if (is.na(fn)) {
+            cat("Can't find wav file for ", identifier, "\n")
+            return(c(0,0,0,0))
+        } else {
+            res = forest(fn, beginTime=start, endTime=end, toFile=FALSE)
+            return(res$fm[nrow(res$fm)/2,])
+        }
+    }
+
+    print(wavmap)
+
+    fm = t(apply(segments, 1, midpoint_fm))
+    fm = data.frame(fm=fm, labels=segments$label, identifier=segments$identifier)
+
+    return(fm)
+}
+
+args = commandArgs(TRUE)
+# args will be like
+# qresult.dat outfile.dat --wavfile a,b,c --identifier A,B,C
+# need to split out wavfile and identifier args on ,
+
+if (length(args) != 6) {
+    print("Wrong number of arguments!")
+    exit(1)
+}
+
+segmentfile = args[1]
+wavfiles = args[4]
+identifiers = args[6]
+outfile = args[2]
+
+# split on comma
+wavfiles = strsplit(wavfiles, ",")[[1]]
+identifiers = strsplit(identifiers, ",")[[1]]
+
+if( length(wavfiles) != length(identifiers)) {
+    print("Lengths of wavfiles and identifiers don't match.")
+    exit(1)
+}
+cat("\nWAVMAP\n")
+wavmap = NULL
+for(i in 1:length(wavfiles)) {
+    wavmap[identifiers[i]] = wavfiles[i]
+}
+
+segments = read.table(segmentfile, header=TRUE)
+
+result = get_fm_at_midpoint(segments, wavmap)
+
+write.table(result, file=outfile, sep="\t", quote=F, row.names=F)