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1 #!/usr/bin/env Rscript
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2
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5
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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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20
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9 make_option(c("-e", "--email"), action="store", dest="email", help="User email address"),
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10 make_option(c("-l", "--long_label"), action="store", dest="long_label", help="Hub long label"),
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11 make_option(c("-n", "--hub_name"), action="store", dest="hub_name", default=NULL, help="Hub name without spaces"),
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12 make_option(c("-p", "--input_dir_para"), action="store", dest="input_dir_para", help="Directory containing .para outputs from IDEAS"),
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13 make_option(c("-q", "--input_dir_state"), action="store", dest="input_dir_state", help="Directory containing .state outputs from IDEAS"),
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20
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14 make_option(c("-s", "--short_label"), action="store", dest="short_label", help="Hub short label"),
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25
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15 make_option(c("-t", "--track_color"), action="store", dest="track_color", default=NULL, help="User specified track color"),
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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("-w", "--output_trackhub"), action="store", dest="output_trackhub", help="Output hub file"),
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18 make_option(c("-x", "--output_trackhub_files_path"), action="store", dest="output_trackhub_files_path", help="Output hub extra files path")
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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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25
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40 track_color <- get_track_color(m, mc);
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41 return(track_color);
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42 }
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43
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22
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44 get_hue = function(val, min=0, max=1) {
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45 if (is.null(val)) {
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46 val = max;
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47 } else if (is.na(val)) {
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48 val = max;
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49 } else if (val < min) {
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50 val = min;
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51 } else if (val > max) {
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52 val = max;
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53 }
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54 return(val);
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55 }
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56
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57 get_track_file_name = function(base_track_file_name, index, ext) {
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58 track_file_name <- paste(base_track_file_name, index, ext, sep=".");
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59 return(track_file_name);
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60 }
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61
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25
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62 get_track_color = function(statemean, markcolor=NULL) {
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22
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63 sm_width = dim(statemean)[1];
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64 sm_height = dim(statemean)[2];
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65 if (length(markcolor) == 0) {
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66 markcolor = rep("", sm_height);
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67 markcolor[order(apply(statemean, 2, sd), decreasing=T)] = hsv((1:sm_height-1)/sm_height, 1, 1);
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68 markcolor = t(col2rgb(markcolor));
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69 }
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70 rg = apply(statemean, 1, range);
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71 mm = NULL;
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22
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72 for (i in 1:sm_width) {
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73 mm = rbind(mm, statemean[i,] - rg[1,i] + 1e-10 / rg[2,i] - rg[1,i] + 1e-10);
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74 }
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75 mm = mm^6;
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76 if(dim(mm)[2] > 1) {
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77 mm = mm / (apply(mm, 1, sum) + 1e-10);
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78 }
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79 mycol = mm%*%markcolor;
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80 s = apply(statemean, 1, max);
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81 s = (s - min(s)) / (max(s) - min(s) + 1e-10);
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22
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82 h = t(apply(mycol, 1, function(x) {rgb2hsv(r=get_hue(x[1]), g=get_hue(x[2]), b=get_hue(x[3]))}));
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83 h[,2] = h[,2] * s;
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84 h = apply(h, 1, function(x) {hsv(x[1], x[2], x[3])});
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85 rt = cbind(apply(t(col2rgb(h)), 1, function(x) {paste(x, collapse=",")}), h);
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86 return(rt);
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87 }
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88
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89 create_primary_html = function(output_trackhub, tracks_dir) {
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90 track_files <- list.files(path=tracks_dir);
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91 s <- paste('<html>\n<head>\n</head>\n<body>\n<ul>\n', sep="");
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92 for (i in 1:length(track_files)) {
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93 track_file <- paste("tracks", track_files[i], sep="/");
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94 s <- paste(s, '<li>\n<a href="', track_file, '">', track_file, '</a>\n</li>', sep="");
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95 }
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96 s <- paste(s, '</ul>\n</body>\n</html>', sep="");
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97 cat(s, file=output_trackhub);
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98 }
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99
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100 create_track = function(input_dir_state, chrom_len_file, base_track_file_name, track_color) {
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101 state_files <- list.files(path=input_dir_state, full.names=TRUE);
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102 genome_size = read.table(chrom_len_file);
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103 g = NULL;
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104 for(i in state_files) {
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105 tg = as.matrix(fread(i));
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106 t = NULL;
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107 for(j in 1:dim(genome_size)[1]) {
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108 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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109 }
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110 if (length(t) > 0) {
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111 tg = tg[-t,];
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112 }
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113 t = which(is.na(match(tg[,2], genome_size[,1]))==T);
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114 if (length(t)>0) {
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115 tg = tg[-t,];
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116 }
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117 g = rbind(g, tg);
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118 }
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119 uchr = sort(unique(as.character(g[,2])));
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120 g1 = NULL;
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121 for(i in uchr) {
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122 t = which(g[,2]==i);
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123 g1 = rbind(g1, g[t[order(as.integer(g[t, 3]))],]);
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124 }
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125 g = NULL;
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126 chr = as.character(g1[,2]);
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127 posst = as.numeric(g1[,3]);
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128 posed = as.numeric(g1[,4]);
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129 state = as.matrix(g1[,5:(dim(g1)[2]-1)]);
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130 state_name = 0:max(state);
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131 L = dim(g1)[1];
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132 n = dim(state)[2];
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133 cells = as.character(colnames(g1)[5:(dim(g1)[2]-1)]);
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134 g1 = NULL;
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135 options(scipen=999);
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136 tt = which(chr[2:L]!=chr[2:L-1]);
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137 tt = c(tt, which(posst[2:L]!=posed[2:L-1]));
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138 tt = sort(unique(tt));
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139 for(i in 1:n) {
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140 tstate = state[,i];
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141 t = c(tt, which(tstate[2:L]!=tstate[2:L-1]));
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142 t = sort(unique(t));
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143 t0 = c(0, t) + 1;
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144 t = c(t, L);
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145 np = cbind(chr[t], posst[t0], posed[t], tstate[t]);
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146 x = cbind(np[,1:3], state_name[as.integer(np[,4])+1], 1000, ".", np[,2:3], track_color[as.numeric(np[,4])+1]);
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147 track_file_name_bed <- get_track_file_name(base_track_file_name, i, "bed");
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148 track_file_name_bigbed <- get_track_file_name(base_track_file_name, i, "bigbed");
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149 write.table(as.matrix(x), track_file_name_bed, quote=F, row.names=F, col.names=F);
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150 system(paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed));
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151 system(paste("rm ", track_file_name_bed));
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152 }
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153 return(cells);
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154 }
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155
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156 create_track_db = function(input_dir_state, chrom_len_file, tracks_dir, hub_name, short_label, long_label, track_color) {
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157 base_track_file_name <- paste(tracks_dir, hub_name, sep="");
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158 cells = create_track(input_dir_state, chrom_len_file, base_track_file_name, track_color);
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159 cell_info = cbind(cells, cells, cells, "#000000");
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160 cell_info = array(cell_info, dim=c(length(cells), 4));
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161 cell_info = as.matrix(cell_info);
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162 track_db = NULL;
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163 for (i in 1:length(cells)) {
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164
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165 ii = which(cells[i] == cell_info[,1]);
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166 if (length(ii) == 0) {
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167 next;
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168 }
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169 ii = ii[1];
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170 # trackDb.txt track entry.
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171 track_db = c(track_db, paste(hub_name, "_track_", i, sep=""));
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172 track_db = c(track_db, "type bigBed");
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173 track_db = c(track_db, paste("bigDataUrl", get_track_file_name(base_track_file_name, i, "bigbed"), sep=" "));
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174 track_db = c(track_db, paste("shortLabel", short_label, sep=" "));
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175 track_db = c(track_db, paste("longLabel", long_label, sep=" "));
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176 track_db = c(track_db, paste("priority", ii));
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177 track_db = c(track_db, "itemRgb on");
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178 track_db = c(track_db, "maxItems 100000");
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179 track_db = c(track_db, paste("color", paste(c(col2rgb(cell_info[ii,4])), collapse=","), sep=" "));
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180 track_db = c(track_db, "visibility dense");
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181 track_db = c(track_db, "");
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182 }
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183 return(track_db);
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184 }
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185
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186 # Create the color scheme.
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187 if (is.null(opt$track_color)) {
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188 track_color <- create_color_scheme(opt$input_dir_para);
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189 else {
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190 track_color <- opt$track_color;
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191 }
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192
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193 # Create the hub.txt output.
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194 contents <- c(paste("hub", opt$hub_name), paste("shortLabel",opt$short_label), paste("longLabel", opt$long_label), paste("genomesFile genomes.txt", sep=""), paste("email", opt$email));
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195 hub_dir <- paste(opt$output_trackhub_files_path, "/", "myHub", "/", sep="");
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196 dir.create(hub_dir, showWarnings=FALSE);
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197 hub_file_path <- paste(hub_dir, "hub.txt", sep="/");
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198 write.table(contents, file=hub_file_path, quote=F, row.names=F, col.names=F);
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199
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200 # Create the genomes.txt output.
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201 contents <- c(paste("genome", opt$build), paste("trackDb ", opt$build, "/", "trackDb.txt", sep=""));
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202 genomes_file_path <- paste(opt$output_trackhub_files_path, "/", "genomes.txt", sep="");
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203 write.table(contents, file=genomes_file_path, quote=F, row.names=F, col.names=F);
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204
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205 # Create the tracks.
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206 tracks_dir <- paste(opt$output_trackhub_files_path, "/", "tracks", "/", sep="");
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207 dir.create(tracks_dir, showWarnings=FALSE);
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208 track_db <- create_track_db(opt$input_dir_state, opt$chrom_len_file, tracks_dir, opt$hub_name, opt$short_label, opt$long_label, track_color);
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209
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210 # Create the trackDb.txt output.
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211 track_db_file_path <- paste(tracks_dir, "trackDb.txt", sep="");
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212 write.table(track_db, file=track_db_file_path, quote=F, row.names=F, col.names=F);
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213
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214 # Create the primary HTML dataset.
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215 create_primary_html(opt$output_trackhub, tracks_dir);
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