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1 # Name: region_motif_intersect.r
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2 # Description: Takes a bed file of target regions and counts intersections
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3 # of each motif (built in rdata database) and target regions.
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4 # Author: Jeremy liu
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5 # Email: jeremy.liu@yale.edu
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6 # Date: 14/07/02
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7 # Note: This script is meant to be invoked with the following command
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8 # R --slave --vanilla -f ./region_motif_intersect.r --args <workingdir> <db> <inbed> <outtab>
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9 # <workingdir> is working directory of galaxy installation
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10 # <db> types: "t" test, "p" pouya, "j" jaspar jolma, "m" mouse
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11 # Dependencies: none
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12
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13 # Auxiliary function to concatenate multiple strings
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14 concat <- function(...) {
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15 input_list <- list(...)
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16 return(paste(input_list, sep="", collapse=""))
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17 }
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18
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19 # Set common and data directories
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20 args <- commandArgs()
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21 workingDir = args[7]
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22 dbDir = concat(workingDir, "/region_motif_db")
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23 dbCode = args[8]
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24 if (dbCode == "t") {
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25 motifDB = concat(dbDir, "/pouya_test_motifs.bed.bgz")
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26 } else if (dbCode == "p") {
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27 motifDB = concat(dbDir, "/pouya_motifs.bed.bgz")
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28 } else if (dbCode == "j") {
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29 motifDB = concat(dbDir, "/jaspar_jolma_motifs.bed.bgz")
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30 } else if (dbCode == "m") {
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31 motifDB = concat(dbDir, "/mm9_motifs.bed.bgz")
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32 } else {
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33 motifDB = concat(dbDir, "/pouya_motifs.bed.bgz")
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34 }
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35
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36 # Set input and reference files, comment to toggle commmand line arguments
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37 inBed = args[9]
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38 outTab = args[10]
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39
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40 # Auxiliary function to read in BED file
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41 read_bed <- function(file) {
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42 return(read.table(file, sep="\t", stringsAsFactors=FALSE))
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43 }
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44
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45 startTime = Sys.time()
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46 cat("Running ... Started at:", format(startTime, "%a %b %d %X %Y"), "...\n")
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47
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48 # Load dependencies
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49 cat("Loading dependencies...\n")
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50 suppressPackageStartupMessages(library(Rsamtools, quietly=TRUE))
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51
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52 # Initializing hash table (as env) with motif names and loading tabix file
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53 cat("Loading motif database and initializing hash table...\n")
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54 motifTable = new.env()
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55 motifTbx <- TabixFile(motifDB)
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56
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57 # Loading input bed file, convert integer columns to numeric, name columns
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58 cat("Loading region file...\n")
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59 regionsDF = read_bed(inBed)
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60 dfTemp = sapply(regionsDF, is.integer)
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61 regionsDF[dfTemp] = lapply(regionsDF[dfTemp], as.numeric)
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62 names(regionsDF)[names(regionsDF) == "V1"] = "chr"
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63 names(regionsDF)[names(regionsDF) == "V2"] = "start"
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64 names(regionsDF)[names(regionsDF) == "V3"] = "end"
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65
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66 # Filtering regions to exclude chromosomes not in motif database
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67 cat("Determining intersection counts...\n")
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68 motifTbxChrs = seqnamesTabix(motifTbx)
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69 regionsDFFilter = subset(regionsDF, chr %in% motifTbxChrs)
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70
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71 # Loading regions into GRanges object and scanning motif tabix database
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72 # Region end is incremented by 1 since scanTabix querying is inclusive for
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73 # position start but exclusive for position end.
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74 param = GRanges(regionsDFFilter$chr, IRanges(regionsDFFilter$start,
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75 end=regionsDFFilter$end + 1))
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76 regionsIntersects = scanTabix(motifTbx, param=param)
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77
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78 # Parsing result list and updating motif count hash table
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79 cat("Parsing result list...\n")
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80 for(regionIntersects in regionsIntersects) {
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81 for(regionIntersect in strsplit(regionIntersects, " ")) {
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82 intersectMotif = strsplit(regionIntersect, "\t")[[1]][4]
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83 if(is.null(motifTable[[intersectMotif]])) {
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84 motifTable[[intersectMotif]] = 1
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85 } else {
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86 motifTable[[intersectMotif]] = motifTable[[intersectMotif]] + 1
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87 }
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88 }
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89 }
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90
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91 # Converting motif count hash table to an integer vector for output
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92 counts = integer(length = length(ls(motifTable)))
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93 names(counts) = ls(motifTable)
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94 for(motifName in ls(motifTable)) {
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95 counts[motifName] = as.integer(motifTable[[motifName]])
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96 }
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97
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98 # Outputting intersection counts to tab delineated file
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99 cat("Outputting to file...\n")
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100 write.table(counts, outTab, quote=FALSE, sep="\t", row.names=TRUE, col.names=FALSE)
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101 cat("Done. Job started at:", format(startTime, "%a %b %d %X %Y."),
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102 "Job ended at:", format(Sys.time(), "%a %b %d %X %Y."), "\n")
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