# HG changeset patch
# User greg
# Date 1513363292 18000
# Node ID d7ab58fe039f5abf30be375a4db251f214ee1fa5
# Parent 8b1c49f2ecaaa6081756bd0e521e372c6cad58c9
Uploaded
diff -r 8b1c49f2ecaa -r d7ab58fe039f ideas_genome_tracks.R
--- a/ideas_genome_tracks.R Thu Dec 14 14:49:54 2017 -0500
+++ b/ideas_genome_tracks.R Fri Dec 15 13:41:32 2017 -0500
@@ -5,17 +5,17 @@
suppressPackageStartupMessages(library("viridisLite"))
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_name"), action="store", dest="hub_name", default=NULL, help="Hub name without spaces"),
- make_option(c("--input_dir_state"), action="store", dest="input_dir_state", help="Directory containing .state outputs from IDEAS"),
- make_option(c("--long_label"), action="store", dest="long_label", help="Hub long label"),
- 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("--short_label"), action="store", dest="short_label", help="Hub short label")
+ 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_name"), action="store", dest="hub_name", default=NULL, help="Hub name without spaces"),
+ make_option(c("--input_dir_state"), action="store", dest="input_dir_state", help="Directory containing .state outputs from IDEAS"),
+ make_option(c("--long_label"), action="store", dest="long_label", help="Hub long label"),
+ 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("--short_label"), action="store", dest="short_label", help="Hub short label")
)
parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
@@ -23,120 +23,120 @@
opt <- args$options
create_primary_html = function(output_trackhub, tracks_dir, build) {
- track_files <- list.files(path=tracks_dir);
- s <- paste('
', sep="\n");
- s <- paste(s, 'Contents of directory ~/myHub/', build, ' required by UCSC TrackHub
\n', sep="");
- s <- paste(s, '\n', sep="")
- for (i in 1:length(track_files)) {
- s <- paste(s, '- ', track_files[i], '
\n', sep="");
- }
- s <- paste(s, '
\n\n', sep="");
- cat(s, file=output_trackhub);
+ track_files <- list.files(path=tracks_dir);
+ s <- paste('', sep="\n");
+ s <- paste(s, 'Contents of directory ~/myHub/', build, ' required by UCSC TrackHub
\n', sep="");
+ s <- paste(s, '\n', sep="")
+ for (i in 1:length(track_files)) {
+ s <- paste(s, '- ', track_files[i], '
\n', sep="");
+ }
+ s <- paste(s, '
\n\n', sep="");
+ cat(s, file=output_trackhub);
}
create_track = function(input_dir_state, chrom_len_file, base_track_file_name) {
- # Create everythin 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);
- 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)]);
- state_name = 0:max(state);
- L = dim(g1)[1];
- 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) {
- 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]);
- 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[as.integer(np[,4])+1], 1000, ".", np[,2:3]);
- write.table(as.matrix(x), track_file_name_bed, quote=F, row.names=F, col.names=F);
- system(paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed));
- system(paste("rm ", track_file_name_bed));
- }
- return(cells);
+ # Create everythin 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);
+ 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)]);
+ state_name = 0:max(state);
+ L = dim(g1)[1];
+ 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) {
+ 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]);
+ 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, "bb");
+ x = cbind(np[, 1:3], state_name[as.integer(np[,4])+1], 1000, ".", np[,2:3]);
+ write.table(as.matrix(x), track_file_name_bed, quote=F, row.names=F, col.names=F);
+ system(paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed));
+ system(paste("rm ", track_file_name_bed));
+ }
+ return(cells);
}
create_track_db = function(galaxy_url, encoded_dataset_id, input_dir_state, build, chrom_len_file, tracks_dir, hub_name, short_label, long_label) {
- # Create a trackDb.txt file that includes each state.
- base_track_file_name <- paste(tracks_dir, hub_name, sep="");
- cells = create_track(input_dir_state, chrom_len_file, base_track_file_name);
- # Create a a character vector of 1024 viridis color hex codes.
- viridis_vector <- viridis(1024, alpha=1, begin=0, end=1, direction=1, option="D");
- colors_used <- vector();
- track_db = NULL;
- for (i in 1:length(cells)) {
- # Generate a random number between 1 and 1024 as
- # the viridis_vector index for the next state color.
- color_index <- sample(1:1024, 1)
- # Make sure the color was not previously chosen.
- while(is.element(color_index, colors_used)) {
- color_index <- sample(1:1024, 1)
- }
- # Append the color to our list of chosen colors.
- append(colors_used, color_index)
- # Get the hex code from viridis_vector.
- viridis_color_hex_code <- viridis_vector[color_index]
- big_data_url <- get_big_data_url(galaxy_url, encoded_dataset_id, tracks_dir, i, build);
- # trackDb.txt track 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", short_label, sep=" "));
- track_db = c(track_db, paste("longLabel", long_label, 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", paste(c(col2rgb(viridis_color_hex_code)), collapse=","), sep=" "));
- track_db = c(track_db, "visibility dense");
- track_db = c(track_db, "");
- }
- return(track_db);
+ # Create a trackDb.txt file that includes each state.
+ base_track_file_name <- paste(tracks_dir, hub_name, sep="");
+ cells = create_track(input_dir_state, chrom_len_file, base_track_file_name);
+ # Create a a character vector of 1024 viridis color hex codes.
+ viridis_vector <- viridis(1024, alpha=1, begin=0, end=1, direction=1, option="D");
+ colors_used <- vector();
+ track_db = NULL;
+ for (i in 1:length(cells)) {
+ # Generate a random number between 1 and 1024 as
+ # the viridis_vector index for the next state color.
+ color_index <- sample(1:1024, 1)
+ # Make sure the color was not previously chosen.
+ while(is.element(color_index, colors_used)) {
+ color_index <- sample(1:1024, 1)
+ }
+ # Append the color to our list of chosen colors.
+ append(colors_used, color_index)
+ # Get the hex code from viridis_vector.
+ viridis_color_hex_code <- viridis_vector[color_index]
+ big_data_url <- get_big_data_url(galaxy_url, encoded_dataset_id, tracks_dir, i, build);
+ # trackDb.txt track 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", short_label, sep=" "));
+ track_db = c(track_db, paste("longLabel", long_label, 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", paste(c(col2rgb(viridis_color_hex_code)), collapse=","), 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)
+ 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_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);
+ track_file_name <- paste(base_track_file_name, index, ext, sep=".");
+ return(track_file_name);
}
# Create the hub.txt output.
@@ -168,4 +168,4 @@
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$build);
\ No newline at end of file
+create_primary_html(opt$output_trackhub, tracks_dir, opt$build);