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comparison region_motif_intersect.r @ 3:cab2db9d058b draft

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author jeremyjliu
date Sat, 16 May 2015 22:35:26 -0400
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2:2538677b6004 3:cab2db9d058b
1 # Name: region_motif_intersect.r
2 # Description: Takes a bed file of target regions and counts intersections
3 # of each motif (in separately installed tabix database) and target regions.
4 # Author: Jeremy Liu
5 # Email: jeremy.liu@yale.edu
6 # Date: 15/02/11
7 # Note: This script can be invoked with the following command
8 # R --slave --vanilla -f ./region_motif_intersect.r --args <db_bgz> <db_tbi> <inbed> <outtab>
9 # Dependencies: region_motif_data_manager, Rsamtools
10
11 # Auxiliary function to concatenate multiple strings
12 concat <- function(...) {
13 input_list <- list(...)
14 return(paste(input_list, sep="", collapse=""))
15 }
16
17 # Retrive motif database path
18 args <- commandArgs()
19 motifDB_bgz = unlist(strsplit(args[7], ','))[1] # Handles duplicate entries in data table
20 motifDB_tbi = unlist(strsplit(args[8], ','))[1] # Just takes the first one
21
22 # Set input and reference files, comment to toggle commmand line arguments
23 inBed = args[9]
24 outTab = args[10]
25
26 # Auxiliary function to read in BED file
27 read_bed <- function(file) {
28 return(read.table(file, sep="\t", stringsAsFactors=FALSE))
29 }
30
31 startTime = Sys.time()
32 cat("Running ... Started at:", format(startTime, "%a %b %d %X %Y"), "...\n")
33
34 # Load dependencies
35 cat("Loading dependencies...\n")
36 suppressPackageStartupMessages(library(Rsamtools, quietly=TRUE)) # NEED TO HANDLE INSTALLATION
37
38 # Initializing hash table (as env) with motif names and loading tabix file
39 cat("Loading motif database and initializing hash table...\n")
40 motifTable = new.env()
41 motifTbx <- TabixFile(motifDB_bgz)
42
43 # Loading input bed file, convert integer columns to numeric, name columns
44 cat("Loading region file...\n")
45 regionsDF = read_bed(inBed)
46 dfTemp = sapply(regionsDF, is.integer)
47 regionsDF[dfTemp] = lapply(regionsDF[dfTemp], as.numeric)
48 names(regionsDF)[names(regionsDF) == "V1"] = "chr"
49 names(regionsDF)[names(regionsDF) == "V2"] = "start"
50 names(regionsDF)[names(regionsDF) == "V3"] = "end"
51
52 # Filtering regions to exclude chromosomes not in motif database
53 cat("Determining intersection counts...\n")
54 motifTbxChrs = seqnamesTabix(motifTbx)
55 regionsDFFilter = subset(regionsDF, chr %in% motifTbxChrs)
56
57 # Loading regions into GRanges object and scanning motif tabix database
58 # Region end is incremented by 1 since scanTabix querying is inclusive for
59 # position start but exclusive for position end.
60 param = GRanges(regionsDFFilter$chr, IRanges(regionsDFFilter$start,
61 end=regionsDFFilter$end + 1))
62 regionsIntersects = scanTabix(motifTbx, param=param)
63
64 # Parsing result list and updating motif count hash table
65 cat("Parsing result list...\n")
66 for(regionIntersects in regionsIntersects) {
67 for(regionIntersect in strsplit(regionIntersects, " ")) {
68 intersectMotif = strsplit(regionIntersect, "\t")[[1]][4]
69 if(is.null(motifTable[[intersectMotif]])) {
70 motifTable[[intersectMotif]] = 1
71 } else {
72 motifTable[[intersectMotif]] = motifTable[[intersectMotif]] + 1
73 }
74 }
75 }
76
77 # Converting motif count hash table to an integer vector for output
78 counts = integer(length = length(ls(motifTable)))
79 names(counts) = ls(motifTable)
80 for(motifName in ls(motifTable)) {
81 counts[motifName] = as.integer(motifTable[[motifName]])
82 }
83
84 # Outputting intersection counts to tab delineated file
85 cat("Outputting to file...\n")
86 write.table(counts, outTab, quote=FALSE, sep="\t", row.names=TRUE, col.names=FALSE)
87 cat("Done. Job started at:", format(startTime, "%a %b %d %X %Y."),
88 "Job ended at:", format(Sys.time(), "%a %b %d %X %Y."), "\n")