forked from mahmoudibrahim/JAMM
-
Notifications
You must be signed in to change notification settings - Fork 1
/
bincalculator.r
222 lines (192 loc) · 6.63 KB
/
bincalculator.r
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
########################################################################
# JAMMv1.0.7rev4 is a peak finder for joint analysis of NGS replicates.
# Copyright (C) 2014-2016 Mahmoud Ibrahim
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Contact: mahmoud.ibrahim@mdc-berlin.de
########################################################################
# =======================
# User-defined variables
# =======================
defaultBins = seq(50, 50*15, by = 50) # default binsize search space, used when fragment length is equal or less than read length
#=======================> DONE!
# ================================
# Required Libraries check & load
# ================================
if ((is.element('parallel', installed.packages()[,1]) == FALSE)) {
stop("R package'parallel' is required. Please install it!")
}
suppressPackageStartupMessages(library("parallel"))
#=======================> DONE!
# =================
# Custom Functions
# =================
#Implements the Shimazaki procedure
shimazaki = function(bedfile, rl, bins, maxIter, filelist, chromSize, type) {
#read in the file data
if (type == "single") {
reads = read.table(bedfile, header = FALSE)
reads = cbind(as.character(reads[[1]]), as.character(reads[[2]]))
}
if (type == "paired") {
reads = read.table(bedfile, header = FALSE)
reads = cbind(as.numeric(reads[[1]]), as.numeric(reads[[2]]))
}
readnum = length(reads[[1]])
o = which(filelist == bedfile)
readlen = rl[o]
jack = o - 1
bins = bins[(1+(jack*15)):(15+(jack*15))]
costs = vector(mode = "numeric", length = length(bins))
#Shimazaki procedure
for (i in 1:length(bins)) {
#construct the counting breaks vector
genomevec = seq(0, chromSize, by = bins[i]);
if (max(genomevec) < chromSize) {
genomevec = append(genomevec, chromSize);
}
#create a vector of read counts
if (type == "single") {
ameirah = sort(c((as.numeric(reads[reads[,2] == "+",,drop = FALSE][,1])), ((as.numeric(reads[reads[,2] == "-",,drop = FALSE][,1])) + readlen - 1)))
}
if (type == "paired") {
ameirah = sort(c((reads[[1]]), (reads[[2]])))
}
ameirah = hist(ameirah, breaks = genomevec, plot = FALSE)
ameirah = ameirah$counts
#get cost function
m = mean(ameirah)
v = (sum((ameirah - m)^2)) / (length(ameirah))
num = ((2*m) - v)
den = ((bins[i]) * readnum)^2
cost = -(log(abs(num)) - log(den))
costs[i] = cost
}
index = which.min(costs)
finbin = bins[index]
return(finbin)
}
#=======================> DONE!
# ==========================
# Parse-in System Variables
# ==========================
args = commandArgs(trailingOnly = TRUE) # Read Arguments from command line
#Set arguments to default values
ibed = NA # input bed file
sFile = NA # chromosome size
storeFile = NA # file to store result
cornum = 1 # number of processors to use
rl = NA # read length
frags = NA # fragment lengths
bins = NA
#Parsing arguments and storing values
for (each.arg in args) {
if (grepl('^-s=',each.arg)) {
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
if (! is.na(arg.split[2]) ) {
sFile <- arg.split[2]
} else {
stop('No chromosome size file')
}
}
if (grepl('^-rl=',each.arg)) {
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
if (! is.na(arg.split[2]) ) {
rl <- arg.split[2]
}
}
if (grepl('^-d=',each.arg)) {
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
if (! is.na(arg.split[2]) ) {
storeFile <- arg.split[2]
} else {
stop('No file to store result')
}
}
if (grepl('^-ibed=',each.arg)) {
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
if (! is.na(arg.split[2]) ) {
ibed <- arg.split[2]
} else {
message('ERROR: The largest chromosome in your chromosome size file (-g) has no reads in one or more of your BED files (-s). I can not calculate the bin size. You can either delete this chromosome from your chromosome size file or specify a bin size using -b parameter!')
quit(status = 1)
}
}
if (grepl('^-p=',each.arg)) {
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
if (! is.na(arg.split[2]) ) {
cornum <- as.numeric(arg.split[2])
} else {
stop('No number of cores given')
}
}
if (grepl('^-f=',each.arg)) {
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
if (! is.na(arg.split[2]) ) {
frags <- arg.split[2]
} else {
stop('No Fragment lengths given')
}
}
if (grepl('^-type=',each.arg)) {
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
if (! is.na(arg.split[2]) ) {
type <- arg.split[2]
} else {
stop('No type given')
}
}
#number of replicates
if (grepl('-nreps=',each.arg)) {
arg.split <- strsplit(each.arg,'=',fixed=TRUE)[[1]]
if (! is.na(arg.split[2]) ) {
nreps <- as.numeric(arg.split[2])
}
}
}
#Read in variables
chromosomes = read.table(sFile, header=FALSE)
chromSize = as.numeric(chromosomes$V2) #chromosome size
chromSize = max(chromSize) #get maximum chrom size
rm(chromosomes)
ibed = strsplit(ibed, ",", fixed = TRUE)[[1]]
if (length(ibed) != nreps) {
message('ERROR: The largest chromosome in your chromosome size file (-g) has no reads in one or more of your BED files (-s). I can not calculate the bin size. You can either delete this chromosome from your chromosome size file or specify a bin size using -b parameter. Exiting!')
quit()
}
rl = as.numeric(strsplit(rl, ",", fixed = TRUE)[[1]])
frags = as.numeric(strsplit(frags, ",", fixed = TRUE)[[1]])
#=======================> DONE!
# ===================================================
# Shimazaki Procedure (Shimazaki and Shinomoto 2007)
# ===================================================
for (i in 1:length(ibed)) {
if (frags[i] > rl[i]) {
minbin = floor(frags[i] / 2)
bins = c(bins, seq(minbin, minbin*15, by = minbin))
} else {
bins = c(bins, defaultBins)
}
}
bins = bins[!is.na(bins)]
bins = mclapply(ibed, shimazaki, rl, bins, maxIter, ibed, chromSize, type = type, mc.cores = cornum)
bins = min(unlist(bins))
#=======================> DONE!
# ==================
# Write Information
# ==================
write(paste0(bins), file = paste0(storeFile, "/binsize.txt"))
message(bins)
#=======================> DONE!