Mercurial > repos > greg > ideas_genome_tracks
view ideas_genome_tracks.R @ 88:3e9e8a7bcba6 draft
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| author | greg |
|---|---|
| date | Wed, 10 Jan 2018 11:10:46 -0500 |
| parents | 60ce288eb52f |
| children | a1242a42050a |
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#!/usr/bin/env Rscript suppressPackageStartupMessages(library("data.table")) suppressPackageStartupMessages(library("optparse")) option_list <- list( make_option(c("--build"), action="store", dest="build", help="Genome build"), make_option(c("--chrom_len_file"), action="store", dest="chrom_len_file", help="Chromosome length file"), make_option(c("--email"), action="store", dest="email", help="User email address"), make_option(c("--galaxy_url"), action="store", dest="galaxy_url", help="Galaxy instance base URL"), make_option(c("--hub_long_label"), action="store", dest="hub_long_label", help="Hub long label"), make_option(c("--hub_name"), action="store", dest="hub_name", default=NULL, help="Hub name without spaces"), make_option(c("--hub_short_label"), action="store", dest="hub_short_label", help="Hub short label"), make_option(c("--input_dir_para"), action="store", dest="input_dir_para", help="Directory containing .para outputs from IDEAS"), make_option(c("--input_dir_state"), action="store", dest="input_dir_state", help="Directory containing .state outputs from IDEAS"), make_option(c("--output_trackhub"), action="store", dest="output_trackhub", help="Output hub file"), make_option(c("--output_trackhub_files_path"), action="store", dest="output_trackhub_files_path", help="Output hub extra files path"), make_option(c("--output_trackhub_id"), action="store", dest="output_trackhub_id", help="Encoded output_trackhub dataset id"), make_option(c("--script_dir"), action="store", dest="script_dir", help="R script source directory"), make_option(c("--state_colors"), action="store", dest="state_colors", default=NULL, help="List of state colors"), make_option(c("--state_indexes"), action="store", dest="state_indexes", default=NULL, help="List of state indexes"), make_option(c("--state_names"), action="store", dest="state_names", default=NULL, help="List of state names") ) parser <- OptionParser(usage="%prog [options] file", option_list=option_list) args <- parse_args(parser, positional_arguments=TRUE) opt <- args$options create_primary_html = function(output_trackhub, tracks_dir, build) { track_files <- list.files(path=tracks_dir); s <- paste('<html><head></head><body>', sep="\n"); s <- paste(s, '<h3>Contents of directory ~/myHub/', build, ' required by UCSC TrackHub</h3>\n', sep=""); s <- paste(s, '<ul>\n', sep="") for (i in 1:length(track_files)) { s <- paste(s, '<li><a href="', 'myHub/', build, "/", track_files[i], '">', track_files[i], '</a></li>\n', sep=""); } s <- paste(s, '</ul>\n</body>\n</html>', sep=""); cat(s, file=output_trackhub); } create_cells = function(input_dir_state, chrom_len_file, base_track_file_name, state_indexes, state_names, state_colors) { # Create everything needed, including the bigbed file, # to render the tracks within the UCSC track hub. state_files = list.files(path=input_dir_state, full.names=TRUE); cell_type_names = get_cell_type_names(state_files[1]); genome_size = read.table(chrom_len_file); g = NULL; for(i in state_files) { tg = as.matrix(fread(i)); t = NULL; for(j in 1:dim(genome_size)[1]) { t = c(t, which(tg[,2]==as.character(genome_size[j, 1]) & as.numeric(tg[,4]) > as.numeric(genome_size[j, 2]))); } if (length(t) > 0) { tg = tg[-t,]; } t = which(is.na(match(tg[,2], genome_size[,1]))==T); if (length(t)>0) { tg = tg[-t,]; } g = rbind(g, tg); } uchr = sort(unique(as.character(g[,2]))); g1 = NULL; for(i in uchr) { t = which(g[,2]==i); g1 = rbind(g1, g[t[order(as.integer(g[t, 3]))],]); } g = NULL; chr = as.character(g1[,2]); posst = as.numeric(g1[,3]); posed = as.numeric(g1[,4]); state = as.matrix(g1[,5:(dim(g1)[2]-1)]); L = dim(g1)[1]; # Here n will be the same length as the # list of cell_type_names defined above. n = dim(state)[2]; cells = as.character(colnames(g1)[5:(dim(g1)[2]-1)]); options(scipen=999); tt = which(chr[2:L]!=chr[2:L-1]); tt = c(tt, which(posst[2:L]!=posed[2:L-1])); tt = sort(unique(tt)); for(i in 1:n) { state_name = cell_type_names[i]; tstate = state[,i]; t = c(tt, which(tstate[2:L]!=tstate[2:L-1])); t = sort(unique(t)); t0 = c(0, t) + 1; t = c(t, L); np = cbind(chr[t], posst[t0], posed[t], tstate[t]); #cat("JJJJJJJ as.numeric(np[,4]: ", as.numeric(np[,4]), "\n"); track_file_name_bed_unsorted <- get_track_file_name(base_track_file_name, i, "bed_unsorted"); track_file_name_bed <- get_track_file_name(base_track_file_name, i, "bed"); track_file_name_bigbed <- get_track_file_name(base_track_file_name, i, "bigbed"); x = cbind(np[, 1:3], state_name, 1000, ".", np[,2:3]); write.table(as.matrix(x), track_file_name_bed_unsorted, quote=F, row.names=F, col.names=F); cmd = paste("LC_COLLATE=C sort -k1,1 -k2,2n < ", track_file_name_bed_unsorted, " > ", track_file_name_bed); system(cmd); cmd = paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed); system(cmd); system(paste("rm ", track_file_name_bed_unsorted)); system(paste("rm ", track_file_name_bed)); } return(cells); } create_track_db = function(galaxy_url, encoded_dataset_id, input_dir_para, input_dir_state, build, chrom_len_file, tracks_dir, hub_name, hub_short_label, hub_long_label, specified_state_indexes, specified_state_names, specified_state_colors) { # Create a trackDb.txt file that includes each state. #cat("\n\n\n\n\nXXXXXXXXXXXXXXXX Entered create_track_db\n"); #cat("specified_state_indexes: ", specified_state_indexes, "\n"); #cat("specified_state_names: ", specified_state_names, "\n"); #cat("specified_state_colors: ", specified_state_colors, "\n"); state_names = c(); state_colors = list(); # Generate the default state names and colors. # IDEAS state indexes are zero based. index = 0; para_files = list.files(path=input_dir_para, full.names=TRUE); #cat("para_files: ", toString(para_files), "\n\n\n"); for (para_file in para_files) { #cat("para_file: ", para_file, "\n"); # Append the default state name. state_names = c(state_names, toString(index)); #cat("\n", index,index,index,index, "state_names: ", state_names, "\n"); # Append the default color codes vector. data_frame = read.table(para_file, comment="!", header=T); # Here specified_state_colors will look something like this: # 248,239,0 254,153,95 255,255,255 245,245,0 #F8EF00 #FE995F #FFFFFF #F5F500 state_color_codes_vector = create_heatmap(data_frame); #cat("state_color_codes_vector: ", state_color_codes_vector, "\n"); #cat("typeof(state_color_codes_vector): ", typeof(state_color_codes_vector), "\n"); #cat("length(state_color_codes_vector): ", length(state_color_codes_vector), "\n"); state_colors[[index + 1]] = state_color_codes_vector; #cat("\n", index,index,index,index, "state_colors: ", state_colors, "\n"); index = index + 1; } #cat("\n\nBBBBBBBB default state_names: ", state_names, "\n"); #cat("BBBBBBBB default typeof(state_names): ", typeof(state_names), "\n"); #cat("BBBBBBBB default length(state_names): ", length(state_names), "\n"); #cat("BBBBBBBB default state_colors: ", toString(state_colors), "\n"); #cat("BBBBBBBB default length(state_colors): ", length(state_colors), "\n\n\n"); if (!is.null(specified_state_indexes)) { # Replace default name with specified name and default # color with specified color for each selected state. # Split specified_state_indexes into a list of strings. index_str = as.character(specified_state_indexes); specified_state_index_items = strsplit(index_str, ",")[[1]]; # Split specified_state_names into a list of strings. name_str = as.character(specified_state_names); specified_state_name_items = strsplit(name_str, ",")[[1]]; # Split specified_state_colors into a list of strings. color_str = as.character(specified_state_colors); specified_state_color_items = strsplit(color_str, ",")[[1]]; # Replace default names and colors. loop_index = 1; for (specified_state_index_item in specified_state_index_items) { #cat("specified_state_index_item: ", specified_state_index_item, "\n"); specified_index = as.integer(specified_state_index_item); #cat("specified_index: ", specified_index, "\n"); # Replace default name with specified name. specified_name = specified_state_name_items[loop_index]; # Handle the special string "use state index". if (identical(specified_name, "use state index")) { specified_name = specified_state_index_item; } #cat("specified_name: ", specified_name, "\n"); #cat("state_names: ", state_names, "\n"); #state_names[specified_index] = specified_name; state_names = replace(state_names, state_names==specified_index, specified_name); #cat("state_names: ", state_names, "\n"); # Replace default color with specified color. #cat("specified_state_color_items[specified_item_index]: ", specified_state_color_items[specified_item_index], "\n"); # FixMe: replacing default state colors is not yet working. #state_colors[specified_index] = specified_state_color_items[loop_index]; #cat("state_colors: ", toString(state_colors), "\n"); loop_index = loop_index + 1; } } #cat("\n\nCCCCCC reset state_names: ", state_names, "\n"); #cat("CCCCCC reset state_colors: ", toString(state_colors), "\n"); #cat("CCCCCC reset length(state_colors): ", length(state_colors), "\n\n\n"); base_track_file_name <- paste(tracks_dir, hub_name, sep=""); cells = create_cells(input_dir_state, chrom_len_file, base_track_file_name, state_indexes, state_names, state_colors); cell_info = cbind(cells, cells, cells, "#000000"); cell_info = array(cell_info, dim=c(length(cells), 4)); cell_info = as.matrix(cell_info); track_db = NULL; for (i in 1:length(cells)) { ii = which(cells[i] == cell_info[,1]); if(length(ii) == 0) { next; } ii = ii[1]; # Get the color for the current state. color_vector = state_colors[i]; #cat("color_vector: ", toString(color_vector), "\n"); # We are handling hte hub label color setting here. # FixMe: Color selection is currently very confusing. I think we may # need to add another color selector for the hub label. The current # approach is to apply the specified color for the state to the hub label # if the list of specified_state_index_items contains the value of i - 1 # since state indexes are zero based. #cat("specified_state_index_items: ", specified_state_index_items, "\n"); #cat("length(specified_state_index_items): ", length(specified_state_index_items), "\n"); state_index = i - 1; #cat("state_index: ", state_index, "\n"); if (state_index %in% specified_state_index_items) { specified_state_color = specified_state_color_items[[i]]; #cat("specified_state_color: ", specified_state_color, "\n"); color = paste(c(col2rgb(specified_state_color)), collapse=","); #cat("color 1: ", color, "\n"); } else { color = paste(c(col2rgb("#FFFFFF")), collapse=",") #cat("color 2: ", color, "\n"); } # Get the bigDataUrl. big_data_url <- get_big_data_url(galaxy_url, encoded_dataset_id, tracks_dir, i, build); # trackDb.txt track hub entry. track_db = c(track_db, paste("track ", hub_name, "_track_", i, sep="")); track_db = c(track_db, "type bigBed"); track_db = c(track_db, paste("bigDataUrl", big_data_url, sep=" ")); track_db = c(track_db, paste("shortLabel", cell_info[ii, 2], sep=" ")); track_db = c(track_db, paste("longLabel", paste(hub_name, cell_info[ii, 3], sep=" "))); track_db = c(track_db, paste("priority", i)); track_db = c(track_db, "itemRgb on"); track_db = c(track_db, "maxItems 100000"); track_db = c(track_db, paste("color", color, sep=" ")); track_db = c(track_db, "visibility dense"); track_db = c(track_db, ""); } return(track_db); } get_big_data_url = function(galaxy_url, encoded_dataset_id, tracks_dir, index, build) { track_files <- list.files(path=tracks_dir, pattern="\\.bigbed"); s <- paste(galaxy_url, 'datasets/', encoded_dataset_id, '/display/myHub/', build, '/', track_files[index], sep=""); return(s) } get_cell_type_names = function(state_file) { # The first line of a state file is a comment # that looks something like this: # ID CHR POSst POSed E001 E002 PosClass # The cell type names are the elemets whose # 1-based indexes start at 5 and end with -1, # which in the above case are E001 and E002. fh = file(state_file,"r"); line = readLines(fh, n=1); close(fh); # Split line into a list of strings. items = strsplit(line, "\\s+")[[1]]; # Extract the cell type names into a list. last_cell_type_name_index = length(items) -1; cell_type_names = c(); for (i in 5:last_cell_type_name_index) { cell_type_names = c(cell_type_names, items[i]); } return(cell_type_names); } get_track_file_name = function(base_track_file_name, index, ext) { track_file_name <- paste(base_track_file_name, index, ext, sep="."); return(track_file_name); } # Create the hub.txt output. hub_name_line <- paste("hub ", opt$hub_name, sep=""); hub_short_label_line <- paste("shortLabel ", opt$hub_short_label, sep=""); hub_long_label_line <- paste("longLabel ", opt$hub_long_label, sep=""); genomes_txt_line <- paste("genomesFile genomes.txt", sep=""); email_line <- paste("email ", opt$email, sep=""); contents <- paste(hub_name_line, hub_short_label_line, hub_long_label_line, genomes_txt_line, email_line, sep="\n"); hub_dir <- paste(opt$output_trackhub_files_path, "/", "myHub", "/", sep=""); dir.create(hub_dir, showWarnings=FALSE); hub_file_path <- paste(hub_dir, "hub.txt", sep=""); write.table(contents, file=hub_file_path, quote=F, row.names=F, col.names=F); # Create the genomes.txt output. genome_line <- paste("genome ", opt$build, sep=""); track_db_line <- paste("trackDb ", opt$build, "/", "trackDb.txt", sep=""); contents <- paste(genome_line, track_db_line, sep="\n"); genomes_file_path <- paste(hub_dir, "genomes.txt", sep=""); write.table(contents, file=genomes_file_path, quote=F, row.names=F, col.names=F); # Create the tracks. heatmap_path <- paste(opt$script_dir, "create_heatmap.R", sep="/"); source(heatmap_path); tracks_dir <- paste(hub_dir, opt$build, "/", sep=""); dir.create(tracks_dir, showWarnings=FALSE); track_db <- create_track_db(opt$galaxy_url, opt$output_trackhub_id, opt$input_dir_para, opt$input_dir_state, opt$build, opt$chrom_len_file, tracks_dir, opt$hub_name, opt$hub_short_label, opt$hub_long_label, opt$state_indexes, opt$state_names, opt$state_colors); # Create the trackDb.txt output. track_db_file_path <- paste(tracks_dir, "trackDb.txt", sep=""); write.table(track_db, file=track_db_file_path, quote=F, row.names=F, col.names=F); # Create the primary HTML dataset. create_primary_html(opt$output_trackhub, tracks_dir, opt$build);