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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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83
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7 make_option(c("--build"), action="store", dest="build", help="Genome build"),
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8 make_option(c("--chrom_len_file"), action="store", dest="chrom_len_file", help="Chromosome length file"),
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9 make_option(c("--email"), action="store", dest="email", help="User email address"),
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10 make_option(c("--galaxy_url"), action="store", dest="galaxy_url", help="Galaxy instance base URL"),
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11 make_option(c("--hub_long_label"), action="store", dest="hub_long_label", help="Hub long label"),
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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("--hub_short_label"), action="store", dest="hub_short_label", help="Hub short label"),
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14 make_option(c("--input_dir_para"), action="store", dest="input_dir_para", help="Directory containing .para outputs from IDEAS"),
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15 make_option(c("--input_dir_state"), action="store", dest="input_dir_state", help="Directory containing .state outputs from IDEAS"),
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16 make_option(c("--output_trackhub"), action="store", dest="output_trackhub", help="Output hub file"),
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17 make_option(c("--output_trackhub_files_path"), action="store", dest="output_trackhub_files_path", help="Output hub extra files path"),
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18 make_option(c("--output_trackhub_id"), action="store", dest="output_trackhub_id", help="Encoded output_trackhub dataset id"),
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19 make_option(c("--script_dir"), action="store", dest="script_dir", help="R script source directory"),
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20 make_option(c("--state_colors"), action="store", dest="state_colors", default=NULL, help="List of state colors"),
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21 make_option(c("--state_indexes"), action="store", dest="state_indexes", default=NULL, help="List of state indexes"),
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22 make_option(c("--state_names"), action="store", dest="state_names", default=NULL, help="List of state names")
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0
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23 )
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24
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25 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
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26 args <- parse_args(parser, positional_arguments=TRUE)
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27 opt <- args$options
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28
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78
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29 create_primary_html = function(output_trackhub, tracks_dir, build) {
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30 track_files <- list.files(path=tracks_dir);
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31 s <- paste('<html><head></head><body>', sep="\n");
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32 s <- paste(s, '<h3>Contents of directory ~/myHub/', build, ' required by UCSC TrackHub</h3>\n', sep="");
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33 s <- paste(s, '<ul>\n', sep="")
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34 for (i in 1:length(track_files)) {
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35 s <- paste(s, '<li><a href="', 'myHub/', build, "/", track_files[i], '">', track_files[i], '</a></li>\n', sep="");
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54
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36 }
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37 s <- paste(s, '</ul>\n</body>\n</html>', sep="");
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38 cat(s, file=output_trackhub);
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20
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39 }
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40
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41 create_cells = function(input_dir_state, chrom_len_file, base_track_file_name, state_indexes, state_names, state_colors) {
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66
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42 # Create everything needed, including the bigbed file,
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43 # to render the tracks within the UCSC track hub.
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44 state_files = list.files(path=input_dir_state, full.names=TRUE);
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45 cell_type_names = get_cell_type_names(state_files[1]);
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54
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46 genome_size = read.table(chrom_len_file);
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47 g = NULL;
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48 for(i in state_files) {
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49 tg = as.matrix(fread(i));
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50 t = NULL;
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51 for(j in 1:dim(genome_size)[1]) {
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52 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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53 }
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54 if (length(t) > 0) {
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55 tg = tg[-t,];
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56 }
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57 t = which(is.na(match(tg[,2], genome_size[,1]))==T);
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58 if (length(t)>0) {
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59 tg = tg[-t,];
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60 }
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61 g = rbind(g, tg);
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62 }
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63 uchr = sort(unique(as.character(g[,2])));
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64 g1 = NULL;
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65 for(i in uchr) {
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66 t = which(g[,2]==i);
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67 g1 = rbind(g1, g[t[order(as.integer(g[t, 3]))],]);
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68 }
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69 g = NULL;
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70 chr = as.character(g1[,2]);
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71 posst = as.numeric(g1[,3]);
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72 posed = as.numeric(g1[,4]);
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73 state = as.matrix(g1[,5:(dim(g1)[2]-1)]);
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74 L = dim(g1)[1];
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75 # Here n will be the same length as the
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76 # list of cell_type_names defined above.
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77 n = dim(state)[2];
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78 cells = as.character(colnames(g1)[5:(dim(g1)[2]-1)]);
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79 options(scipen=999);
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80 tt = which(chr[2:L]!=chr[2:L-1]);
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81 tt = c(tt, which(posst[2:L]!=posed[2:L-1]));
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82 tt = sort(unique(tt));
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83 for(i in 1:n) {
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83
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84 state_name = cell_type_names[i];
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85 tstate = state[,i];
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86 t = c(tt, which(tstate[2:L]!=tstate[2:L-1]));
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87 t = sort(unique(t));
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88 t0 = c(0, t) + 1;
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89 t = c(t, L);
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90 np = cbind(chr[t], posst[t0], posed[t], tstate[t]);
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91 track_file_name_bed_unsorted <- get_track_file_name(base_track_file_name, i, "bed_unsorted");
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92 track_file_name_bed <- get_track_file_name(base_track_file_name, i, "bed");
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93 track_file_name_bigbed <- get_track_file_name(base_track_file_name, i, "bigbed");
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94 x = cbind(np[, 1:3], state_name, 1000, ".", np[,2:3]);
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95 write.table(as.matrix(x), track_file_name_bed_unsorted, quote=F, row.names=F, col.names=F);
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96 cmd = paste("LC_COLLATE=C sort -k1,1 -k2,2n < ", track_file_name_bed_unsorted, " > ", track_file_name_bed);
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97 system(cmd);
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98 cmd = paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed);
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99 system(cmd);
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100 system(paste("rm ", track_file_name_bed_unsorted));
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101 system(paste("rm ", track_file_name_bed));
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102 }
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103 return(cells);
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104 }
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105
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106 create_track_db = function(galaxy_url, encoded_dataset_id, input_dir_para, input_dir_state, build, chrom_len_file,
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107 tracks_dir, hub_name, hub_short_label, hub_long_label, state_indexes, state_names, state_colors) {
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108 # Create a trackDb.txt file that includes each state.
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109 s_indexes = c();
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110 s_names = c();
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111 s_colors = c();
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112 if (is.null(state_indexes)) {
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113 # Generate state colors automatically.
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114 index = 0;
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115 para_files = list.files(path=input_dir_para, full.names=TRUE);
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116 for (para_file in para_files) {
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117 data_frame = read.table(para_file, comment="!", header=T);
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118 color_hex_code = create_heatmap(data_frame);
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119 s_indexes = c(s_indexes, index);
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120 s_names = c(s_names, toString(index));
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121 s_colors = c(s_colors, color_hex_code);
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122 }
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123 } else {
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124 # Split state_indexes into a list of integers.
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125 index_str = as.character(state_indexes);
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126 items = strsplit(index_str, ",")
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127 for (item in items) {
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128 s_indexes = c(s_indexes, as.integer(item));
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129 }
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130 # Split state_names into a list of strings.
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131 name_str = as.character(state_names);
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132 items = strsplit(name_str, ",");
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133 item_index = 0;
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134 for (item in items) {
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135 item_index = item_index + 1;
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136 # Handle the special string "use state index".
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137 if (identical(item, "use state index")) {
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138 item = s_indexes[item_index];
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139 }
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140 s_names = c(s_names, item);
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141 }
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142 # Split state_colors into a list of strings.
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143 color_str = as.character(state_colors);
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144 items = strsplit(color_str, ",");
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145 for (item in items) {
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146 s_colors = c(s_colors, item);
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147 }
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148 }
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149 base_track_file_name <- paste(tracks_dir, hub_name, sep="");
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150 cells = create_cells(input_dir_state, chrom_len_file, base_track_file_name, s_indexes, s_names, s_colors);
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151 cell_info = cbind(cells, cells, cells, "#000000");
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152 cell_info = array(cell_info, dim=c(length(cells), 4));
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153 cell_info = as.matrix(cell_info);
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154 track_db = NULL;
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155 for (i in 1:length(cells)) {
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156 ii = which(cells[i] == cell_info[,1]);
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157 if(length(ii) == 0) {
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158 next;
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159 }
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160 ii = ii[1];
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71
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161 # Get the color for the current state.
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162 color <- paste(c(col2rgb(s_colors[i])), collapse=",");
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163 # Get the bigDataUrl.
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164 big_data_url <- get_big_data_url(galaxy_url, encoded_dataset_id, tracks_dir, i, build);
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165 # trackDb.txt track hub entry.
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166 track_db = c(track_db, paste("track ", hub_name, "_track_", i, sep=""));
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167 track_db = c(track_db, "type bigBed");
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168 track_db = c(track_db, paste("bigDataUrl", big_data_url, sep=" "));
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169 track_db = c(track_db, paste("shortLabel", cell_info[ii, 2], sep=" "));
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170 track_db = c(track_db, paste("longLabel", paste(hub_name, cell_info[ii, 3], sep=" ")));
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171 track_db = c(track_db, paste("priority", i));
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172 track_db = c(track_db, "itemRgb on");
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173 track_db = c(track_db, "maxItems 100000");
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174 track_db = c(track_db, paste("color", color, sep=" "));
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175 track_db = c(track_db, "visibility dense");
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176 track_db = c(track_db, "");
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177 }
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178 return(track_db);
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179 }
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180
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181 get_big_data_url = function(galaxy_url, encoded_dataset_id, tracks_dir, index, build) {
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182 track_files <- list.files(path=tracks_dir, pattern="\\.bigbed");
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183 s <- paste(galaxy_url, 'datasets/', encoded_dataset_id, '/display/myHub/', build, '/', track_files[index], sep="");
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184 return(s)
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185 }
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186
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187 get_cell_type_names = function(state_file) {
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188 # The first line of a state file is a comment
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189 # that looks something like this:
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190 # ID CHR POSst POSed E001 E002 PosClass
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191 # The cell type names are the elemets whose
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192 # 1-based indexes start at 5 and end with -1,
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193 # which in the above case are E001 and E002.
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194 fh = file(state_file,"r");
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195 line = readLines(fh, n=1);
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196 close(fh);
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197 # Split line into a list of strings.
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198 items = strsplit(line, "\\s+")[[1]];
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199 # Extract the cell type names into a list.
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200 last_cell_type_name_index = length(items) -1;
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201 cell_type_names = c();
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202 for (i in 5:last_cell_type_name_index) {
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203 cell_type_names = c(cell_type_names, items[i]);
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204 }
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205 return(cell_type_names);
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206 }
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207
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208 get_track_file_name = function(base_track_file_name, index, ext) {
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209 track_file_name <- paste(base_track_file_name, index, ext, sep=".");
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210 return(track_file_name);
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211 }
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212
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213 # Create the hub.txt output.
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214 hub_name_line <- paste("hub ", opt$hub_name, sep="");
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215 hub_short_label_line <- paste("shortLabel ", opt$hub_short_label, sep="");
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216 hub_long_label_line <- paste("longLabel ", opt$hub_long_label, sep="");
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217 genomes_txt_line <- paste("genomesFile genomes.txt", sep="");
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218 email_line <- paste("email ", opt$email, sep="");
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219 contents <- paste(hub_name_line, hub_short_label_line, hub_long_label_line, genomes_txt_line, email_line, sep="\n");
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220 hub_dir <- paste(opt$output_trackhub_files_path, "/", "myHub", "/", sep="");
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221 dir.create(hub_dir, showWarnings=FALSE);
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222 hub_file_path <- paste(hub_dir, "hub.txt", sep="");
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223 write.table(contents, file=hub_file_path, quote=F, row.names=F, col.names=F);
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224
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225 # Create the genomes.txt output.
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226 genome_line <- paste("genome ", opt$build, sep="");
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227 track_db_line <- paste("trackDb ", opt$build, "/", "trackDb.txt", sep="");
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228 contents <- paste(genome_line, track_db_line, sep="\n");
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229 genomes_file_path <- paste(hub_dir, "genomes.txt", sep="");
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230 write.table(contents, file=genomes_file_path, quote=F, row.names=F, col.names=F);
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231
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232 # Create the tracks.
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233 heatmap_path <- paste(opt$script_dir, "create_heatmap.R", sep="/");
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234 source(heatmap_path);
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235 tracks_dir <- paste(hub_dir, opt$build, "/", sep="");
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236 dir.create(tracks_dir, showWarnings=FALSE);
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237 track_db <- create_track_db(opt$galaxy_url, opt$output_trackhub_id, opt$input_dir_para, opt$input_dir_state, opt$build,
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238 opt$chrom_len_file, tracks_dir, opt$hub_name, opt$hub_short_label, opt$hub_long_label, opt$state_indexes,
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239 opt$state_names, opt$state_colors);
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240
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241 # Create the trackDb.txt output.
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242 track_db_file_path <- paste(tracks_dir, "trackDb.txt", sep="");
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243 write.table(track_db, file=track_db_file_path, quote=F, row.names=F, col.names=F);
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244
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245 # Create the primary HTML dataset.
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246 create_primary_html(opt$output_trackhub, tracks_dir, opt$build);
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