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1 #!/usr/bin/env Rscript
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2
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3 suppressPackageStartupMessages(library("data.table"))
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4 suppressPackageStartupMessages(library("optparse"))
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5
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6 option_list <- list(
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7 make_option(c("-b", "--build"), action="store", dest="build", help="Genome build"),
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8 make_option(c("-c", "--chrom_len_file"), action="store", dest="chrom_len_file", help="Chromosome length file"),
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9 make_option(c("-d", "--header"), action="store", dest="header", default=NULL, help="Track header"),
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10 make_option(c("-e", "--state_name"), action="store", dest="state_name", help="State name"),
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11 make_option(c("-f", "--hub_id"), action="store", dest="hub_id", help="Not sure what this is"),
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12 make_option(c("-i", "--cell_info"), action="store", dest="cell_info", default=NULL, help="Not sure what this is"),
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13 make_option(c("-n", "--hub_name"), action="store", dest="hub_name", default=NULL, help="Not sure what this is"),
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14 make_option(c("-p", "--input_dir_para"), action="store", dest="input_dir_para", help="Directory containing .para outputs from IDEAS"),
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15 make_option(c("-q", "--input_dir_state"), action="store", dest="input_dir_state", help="Directory containing .state outputs from IDEAS"),
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16 make_option(c("-u", "--output_track_db"), action="store", dest="output_track_db", help="Output track db file"),
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17 make_option(c("-v", "--output_build"), action="store", dest="output_build", help="Output genome build file"),
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18 make_option(c("-w", "--output_hub"), action="store", dest="output_hub", help="Output hub file")
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19 )
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20
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21 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
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22 args <- parse_args(parser, positional_arguments=TRUE)
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23 opt <- args$options
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24
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25 create_color_scheme = function(input_dir_para) {
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26 # Create the color scheme.
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27 para_files <- list.files(path=input_dir_para, full.names=TRUE);
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28 mc = NULL;
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29 x = read.table(para_files[1], comment="!", nrows=1);
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30 l = as.integer(regexpr("\\*", as.matrix(x)));
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31 l = min(which(l>0)) - 2;
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32 x = as.matrix(read.table(para_files[1]));
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33 if (length(para_files) > 1) {
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34 for (i in 2:length(para_files)) {
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35 x = x + as.matrix(read.table(para_files[i]));
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36 }
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37 }
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38 p = x[,1] / sum(x[,1]);
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39 m = array(as.matrix(x[,1:l+1] / x[,1]), dim=c(dim(x)[1], l));
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40 state_color <- get_state_color(m, mc);
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41 state_color
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42 }
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43
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44 get_state_color = function(statemean, markcolor=NULL)
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45 {
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46 if (length(markcolor) == 0) {
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47 markcolor = rep("", dim(statemean)[2]);
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48 markcolor[order(apply(statemean, 2, sd), decreasing=T)] = hsv((1:dim(statemean)[2]-1)/dim(statemean)[2], 1, 1);
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49 markcolor = t(col2rgb(markcolor));
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50 }
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51 rg = apply(statemean, 1, range);
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52 mm = NULL;
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53 for(i in 1:dim(statemean)[1]) {
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54 mm = rbind(mm, (statemean[i,]-rg[1,i])/(rg[2,i]-rg[1,i]+1e-10));
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55 }
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56 mm = mm^6;
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57 mm = mm / (apply(mm, 1, sum) + 1e-10);
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58 mycol = mm%*%markcolor;
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59 s = apply(statemean, 1, max);
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60 s = (s - min(s)) / (max(s) - min(s) + 1e-10);
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61 h = t(apply(mycol, 1, function(x) {rgb2hsv(x[1], x[2], x[3])}));
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62 h[,2] = h[,2] * s;
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63 h = apply(h, 1, function(x) {hsv(x[1], x[2], x[3])});
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64 rt = cbind(apply(t(col2rgb(h)), 1, function(x) {paste(x, collapse=",")}), h);
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65 return(rt);
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66 }
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67
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68 create_track = function(input_dir_state, chrom_len_file, outpref, state_color, header, state_name) {
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69 state_files <- list.files(path=input_dir_state, full.names=TRUE);
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70 genome_size = read.table(chrom_len_file);
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71 g = NULL;
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72 for(i in state_files) {
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73 tg = as.matrix(fread(i));
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74 t = NULL;
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75 for(j in 1:dim(genome_size)[1]) {
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76 t = c(t, which(tg[,2]==as.character(genome_size[j, 1]) & as.numeric(tg[,4]) > as.numeric(genome_size[j, 2])));
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77 }
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78 if (length(t) > 0) {
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79 tg = tg[-t,];
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80 }
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81 t = which(is.na(match(tg[,2], genome_size[,1]))==T);
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82 if (length(t)>0) {
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83 tg = tg[-t,];
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84 }
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85 g = rbind(g, tg);
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86 }
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87 uchr = sort(unique(as.character(g[,2])));
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88 g1 = NULL;
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89 for(i in uchr) {
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90 t = which(g[,2]==i);
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91 g1 = rbind(g1, g[t[order(as.integer(g[t, 3]))],]);
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92 }
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93 g = NULL;
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94 chr = as.character(g1[,2]);
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95 posst = as.numeric(g1[,3]);
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96 posed = as.numeric(g1[,4]);
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97 state = as.matrix(g1[,5:(dim(g1)[2]-1)]);
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98 if (length(state_name)==0) {
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99 state_name=0:max(state);
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100 }
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101 L = dim(g1)[1];
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102 n = dim(state)[2];
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103 if (length(header) > 0) {
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104 colnames(g1) = header;
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105 }
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106 cells = as.character(colnames(g1)[5:(dim(g1)[2]-1)]);
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107 g1 = NULL;
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108 options(scipen=999);
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109 tt = which(chr[2:L]!=chr[2:L-1]);
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110 tt = c(tt,which(posst[2:L]!=posed[2:L-1]));
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111 tt = sort(unique(tt));
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112 for(i in 1:n) {
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113 tstate = state[,i];
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114 t = c(tt, which(tstate[2:L]!=tstate[2:L-1]));
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115 t = sort(unique(t));
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116 t0 = c(0, t) + 1;
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117 t = c(t, L);
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118 np = cbind(chr[t], posst[t0], posed[t], tstate[t]);
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119 x = cbind(np[,1:3], state_name[as.integer(np[,4])+1], 1000, ".", np[,2:3], state_color[as.numeric(np[,4])+1]);
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120 write.table(as.matrix(x), paste(outpref, i, "bed1", sep="."), quote=F, row.names=F, col.names=F);
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121 system(paste("bedToBigBed ", outpref, ".", i, ".bed1 ", chrom_len_file, " ", outpref, ".", i, ".bb", sep=""));
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122 system(paste("rm ", paste(outpref, i, "bed1", sep=".")));
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123 }
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124 return(cells);
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125 }
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126
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127 create_track_db = function(input_dir_state, chrom_len_file, track_file_name, state_color, header, state_name, hub_name, cell_info) {
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128 cells = create_track(input_dir_state, chrom_len_file, track_file_name, state_color, header, state_name);
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129 if (length(cell_info) == 0) {
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130 cell_info = cbind(cells, cells, cells, "#000000");
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131 cell_info = array(cell_info, dim=c(length(cells), 4));
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132 }
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133 cell_info = as.matrix(cell_info);
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134 track_db = NULL;
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135 for(i in 1:length(cells)) {
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136 ii = which(cells[i] == cell_info[,1]);
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137 if (length(ii) == 0) {
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138 next;
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139 }
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140 ii = ii[1];
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141 track_db = c(track_db, paste("track bigBed", i, sep=""));
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142 track_db = c(track_db, paste("priority", ii));
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143 track_db = c(track_db, "type bigBed 9 .");
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144 track_db = c(track_db, "itemRgb on");
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145 track_db = c(track_db, "maxItems 100000");
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146 track_db = c(track_db, paste("shortLabel", cell_info[ii, 2]));
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147 track_db = c(track_db, paste("longLabel", paste(hub_name, cell_info[ii, 3])));
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148 track_db = c(track_db, paste("color", paste(c(col2rgb(cell_info[ii, 4])), collapse=",")));
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149 track_db = c(track_db, "visibility dense");
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150 track_db = c(track_db, "");
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151 }
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152 }
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153
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154 if (length(opt$hub_name) == 0) {
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155 hub_name = opt$hub_id;
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156 }
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157
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158 # Create the tracks output directory.
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159 tracks_output_dir = paste("tracks_", opt$hub_id, "/", sep="");
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160 dir.create(tracks_output_dir, showWarnings=FALSE);
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161
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162 # Create the color scheme.
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163 state_color <- create_color_scheme(opt$input_dir_para);
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164
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165 # Create the tracks.
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166 track_db <- create_track_db(opt$input_dir_state, opt$chrom_len_file, paste(tracks_output_dir, opt$hub_id, sep=""), state_color, opt$header, opt$state_name, opt$hub_name, opt$cell_info);
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167
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168 # Write the outputs.
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169 write.table(track_db, opt$output_track_db, quote=F, row.names=F, col.names=F);
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170 write.table(c(paste("genome", opt$build), opt$output_build), paste(tracks_output_dir, "genomes_", opt$hub_id, ".txt", sep=""), quote=F, row.names=F, col.names=F);
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171 write.table(c(paste("hub", opt$hub_id), paste("shortLabel", opt$hub_id), paste("longLabel", opt$hub_name), paste("genomesFile genomes_", opt$hub_id, ".txt", sep=""), "email yzz2 at psu.edu"), opt$output_hub, quote=F, row.names=F, col.names=F);
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