Mercurial > repos > stevecassidy > wrassp

annotate get_fm_at_midpoint.R @ 1:dbcf9bc275e3 draft

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planemo upload commit 063e049d569aeb45e1008cbf044f2dad850eca3d-dirty
author stevecassidy
date Wed, 07 Dec 2016 19:10:51 -0500
parents 6d6dc275b107
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1
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2 library(wrassp)
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3
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4 get_fm_at_midpoint <- function(segments, wavmap) {
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5 midpoint_fm <- function(row) {
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6 start = as.numeric(row[1])
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7 end = as.numeric(row[2])
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8 identifier = row[5]
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9 fn = wavmap[identifier]
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10 if (is.na(fn)) {
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11 cat("Can't find wav file for ", identifier, "\n")
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12 return(c(0,0,0,0))
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13 } else {
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14 res = forest(fn, beginTime=start, endTime=end, toFile=FALSE)
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15 return(res$fm[nrow(res$fm)/2,])
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16 }
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17 }
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19 print(wavmap)
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20
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21 fm = t(apply(segments, 1, midpoint_fm))
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22 fm = data.frame(fm=fm, labels=segments$label, identifier=segments$identifier)
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23
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24 return(fm)
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25 }
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27 args = commandArgs(TRUE)
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28 # args will be like
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29 # qresult.dat outfile.dat --wavfile a,b,c --identifier A,B,C
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30 # need to split out wavfile and identifier args on ,
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32 if (length(args) != 6) {
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33 print("Wrong number of arguments!")
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34 exit(1)
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35 }
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36
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37 segmentfile = args[1]
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38 wavfiles = args[4]
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39 identifiers = args[6]
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40 outfile = args[2]
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41
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42 # split on comma
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43 wavfiles = strsplit(wavfiles, ",")[[1]]
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44 identifiers = strsplit(identifiers, ",")[[1]]
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45
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46 if( length(wavfiles) != length(identifiers)) {
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47 print("Lengths of wavfiles and identifiers don't match.")
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48 exit(1)
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49 }
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50 cat("\nWAVMAP\n")
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51 wavmap = NULL
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52 for(i in 1:length(wavfiles)) {
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53 wavmap[identifiers[i]] = wavfiles[i]
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54 }
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56 segments = read.table(segmentfile, header=TRUE)
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57
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58 result = get_fm_at_midpoint(segments, wavmap)
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60 write.table(result, file=outfile, sep="\t", quote=F, row.names=F)