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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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47
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5 suppressPackageStartupMessages(library("viridisLite"))
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6
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7 option_list <- list(
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54
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8 make_option(c("--build"), action="store", dest="build", help="Genome build"),
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9 make_option(c("--chrom_len_file"), action="store", dest="chrom_len_file", help="Chromosome length file"),
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10 make_option(c("--email"), action="store", dest="email", help="User email address"),
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11 make_option(c("--galaxy_url"), action="store", dest="galaxy_url", help="Galaxy instance base URL"),
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12 make_option(c("--hub_name"), action="store", dest="hub_name", default=NULL, help="Hub name without spaces"),
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13 make_option(c("--input_dir_state"), action="store", dest="input_dir_state", help="Directory containing .state outputs from IDEAS"),
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14 make_option(c("--long_label"), action="store", dest="long_label", help="Hub long label"),
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15 make_option(c("--output_trackhub"), action="store", dest="output_trackhub", help="Output hub file"),
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16 make_option(c("--output_trackhub_files_path"), action="store", dest="output_trackhub_files_path", help="Output hub extra files path"),
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17 make_option(c("--output_trackhub_id"), action="store", dest="output_trackhub_id", help="Encoded output_trackhub dataset id"),
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18 make_option(c("--short_label"), action="store", dest="short_label", help="Hub short label")
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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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39
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25 create_primary_html = function(output_trackhub, tracks_dir, build) {
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26 track_files <- list.files(path=tracks_dir);
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27 s <- paste('<html><head></head><body>', sep="\n");
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28 s <- paste(s, '<h3>Contents of directory ~/myHub/', build, ' required by UCSC TrackHub</h3>\n', sep="");
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29 s <- paste(s, '<ul>\n', sep="")
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30 for (i in 1:length(track_files)) {
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31 s <- paste(s, '<li><a href="', 'myHub/', build, "/", track_files[i], '">', track_files[i], '</a></li>\n', sep="");
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32 }
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33 s <- paste(s, '</ul>\n</body>\n</html>', sep="");
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34 cat(s, file=output_trackhub);
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20
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35 }
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36
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37 create_track = function(input_dir_state, chrom_len_file, base_track_file_name) {
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54
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38 # Create everythin needed, including the bigbed file,
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39 # to render the tracks within the UCSC track hub.
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40 state_files <- list.files(path=input_dir_state, full.names=TRUE);
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41 genome_size = read.table(chrom_len_file);
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42 g = NULL;
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43 for(i in state_files) {
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44 tg = as.matrix(fread(i));
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45 t = NULL;
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46 for(j in 1:dim(genome_size)[1]) {
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47 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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48 }
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49 if (length(t) > 0) {
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50 tg = tg[-t,];
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51 }
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52 t = which(is.na(match(tg[,2], genome_size[,1]))==T);
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53 if (length(t)>0) {
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54 tg = tg[-t,];
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55 }
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56 g = rbind(g, tg);
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57 }
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58 uchr = sort(unique(as.character(g[,2])));
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59 g1 = NULL;
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60 for(i in uchr) {
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61 t = which(g[,2]==i);
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62 g1 = rbind(g1, g[t[order(as.integer(g[t, 3]))],]);
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63 }
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64 g = NULL;
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65 chr = as.character(g1[,2]);
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66 posst = as.numeric(g1[,3]);
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67 posed = as.numeric(g1[,4]);
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68 state = as.matrix(g1[,5:(dim(g1)[2]-1)]);
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69 state_name = 0:max(state);
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70 L = dim(g1)[1];
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71 n = dim(state)[2];
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72 cells = as.character(colnames(g1)[5:(dim(g1)[2]-1)]);
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73 options(scipen=999);
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74 tt = which(chr[2:L]!=chr[2:L-1]);
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75 tt = c(tt, which(posst[2:L]!=posed[2:L-1]));
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76 tt = sort(unique(tt));
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77 for(i in 1:n) {
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78 tstate = state[,i];
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79 t = c(tt, which(tstate[2:L]!=tstate[2:L-1]));
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80 t = sort(unique(t));
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81 t0 = c(0, t) + 1;
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82 t = c(t, L);
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83 np = cbind(chr[t], posst[t0], posed[t], tstate[t]);
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84 track_file_name_bed_unsorted <- get_track_file_name(base_track_file_name, i, "bed_unsorted");
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85 track_file_name_bed <- get_track_file_name(base_track_file_name, i, "bed");
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86 track_file_name_bigbed <- get_track_file_name(base_track_file_name, i, "bigbed");
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87 x = cbind(np[, 1:3], state_name[as.integer(np[,4])+1], 1000, ".", np[,2:3]);
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88 write.table(as.matrix(x), track_file_name_bed_unsorted, quote=F, row.names=F, col.names=F);
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89 cmd = paste("LC_COLLATE=C sort -k1,1 -k2,2n < ", track_file_name_bed_unsorted, " > ", track_file_name_bed);
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90 system(cmd);
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91 cmd = paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed);
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92 system(cmd);
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93 system(paste("rm ", track_file_name_bed_unsorted));
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94 system(paste("rm ", track_file_name_bed));
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54
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95 }
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96 return(cells);
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97 }
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98
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99 create_track_db = function(galaxy_url, encoded_dataset_id, input_dir_state, build, chrom_len_file, tracks_dir, hub_name, short_label, long_label) {
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100 # Create a trackDb.txt file that includes each state.
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101 base_track_file_name <- paste(tracks_dir, hub_name, sep="");
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102 cells = create_track(input_dir_state, chrom_len_file, base_track_file_name);
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103 # Create a a character vector of 1024 viridis color hex codes.
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104 viridis_vector <- viridis(1024, alpha=1, begin=0, end=1, direction=1, option="D");
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105 colors_used <- vector();
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106 track_db = NULL;
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107 for (i in 1:length(cells)) {
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108 # Generate a random number between 1 and 1024 as
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109 # the viridis_vector index for the next state color.
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110 color_index <- sample(1:1024, 1)
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111 # Make sure the color was not previously chosen.
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112 while(is.element(color_index, colors_used)) {
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113 color_index <- sample(1:1024, 1)
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114 }
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115 # Append the color to our list of chosen colors.
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116 append(colors_used, color_index)
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117 # Get the hex code from viridis_vector.
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118 viridis_color_hex_code <- viridis_vector[color_index]
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119 big_data_url <- get_big_data_url(galaxy_url, encoded_dataset_id, tracks_dir, i, build);
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120 # trackDb.txt track entry.
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121 track_db = c(track_db, paste("track ", hub_name, "_track_", i, sep=""));
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122 track_db = c(track_db, "type bigBed");
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123 track_db = c(track_db, paste("bigDataUrl", big_data_url, sep=" "));
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124 track_db = c(track_db, paste("shortLabel", short_label, sep=" "));
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125 track_db = c(track_db, paste("longLabel", long_label, sep=" "));
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126 track_db = c(track_db, paste("priority", i));
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127 track_db = c(track_db, "itemRgb on");
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128 track_db = c(track_db, "maxItems 100000");
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129 track_db = c(track_db, paste("color", paste(c(col2rgb(viridis_color_hex_code)), collapse=","), sep=" "));
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130 track_db = c(track_db, "visibility dense");
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131 track_db = c(track_db, "");
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132 }
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133 return(track_db);
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134 }
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135
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136 get_big_data_url = function(galaxy_url, encoded_dataset_id, tracks_dir, index, build) {
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137 track_files <- list.files(path=tracks_dir, pattern="\\.bigbed");
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138 s <- paste(galaxy_url, 'datasets/', encoded_dataset_id, '/display/myHub/', build, '/', track_files[index], sep="");
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139 return(s)
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140 }
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141
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142 get_track_file_name = function(base_track_file_name, index, ext) {
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143 track_file_name <- paste(base_track_file_name, index, ext, sep=".");
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144 return(track_file_name);
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145 }
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146
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147 # Create the hub.txt output.
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148 hub_name_line <- paste("hub ", opt$hub_name, sep="");
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149 short_label_line <- paste("shortLabel ", opt$short_label, sep="");
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150 long_label_line <- paste("longLabel ", opt$long_label, sep="");
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151 genomes_txt_line <- paste("genomesFile genomes.txt", sep="");
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39
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152 email_line <- paste("email ", opt$email, sep="");
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153 contents <- paste(hub_name_line, short_label_line, long_label_line, genomes_txt_line, email_line, sep="\n");
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154 hub_dir <- paste(opt$output_trackhub_files_path, "/", "myHub", "/", sep="");
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155 dir.create(hub_dir, showWarnings=FALSE);
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156 hub_file_path <- paste(hub_dir, "hub.txt", sep="");
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157 write.table(contents, file=hub_file_path, quote=F, row.names=F, col.names=F);
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158
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159 # Create the genomes.txt output.
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160 genome_line <- paste("genome ", opt$build, sep="");
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161 track_db_line <- paste("trackDb ", opt$build, "/", "trackDb.txt", sep="");
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162 contents <- paste(genome_line, track_db_line, sep="\n");
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163 genomes_file_path <- paste(hub_dir, "genomes.txt", sep="");
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164 write.table(contents, file=genomes_file_path, quote=F, row.names=F, col.names=F);
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165
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166 # Create the tracks.
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167 tracks_dir <- paste(hub_dir, opt$build, "/", sep="");
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168 dir.create(tracks_dir, showWarnings=FALSE);
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169 track_db <- create_track_db(opt$galaxy_url, opt$output_trackhub_id, opt$input_dir_state, opt$build, opt$chrom_len_file, tracks_dir, opt$hub_name, opt$short_label, opt$long_label);
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170
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171 # Create the trackDb.txt output.
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172 track_db_file_path <- paste(tracks_dir, "trackDb.txt", sep="");
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173 write.table(track_db, file=track_db_file_path, quote=F, row.names=F, col.names=F);
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174
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175 # Create the primary HTML dataset.
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176 create_primary_html(opt$output_trackhub, tracks_dir, opt$build);
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