# HG changeset patch
# User greg
# Date 1515005957 18000
# Node ID 8c4549f123da3d0049e69e64c7929fc91e8a120e
# Parent a3bd0cecdeb27e4de945e18202c8fba772b17afd
Uploaded
diff -r a3bd0cecdeb2 -r 8c4549f123da ideas_genome_tracks.R
--- a/ideas_genome_tracks.R Wed Jan 03 13:59:09 2018 -0500
+++ b/ideas_genome_tracks.R Wed Jan 03 13:59:17 2018 -0500
@@ -8,36 +8,39 @@
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("--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("--script_dir"), action="store", dest="script_dir", help="R script source directory"),
- make_option(c("--short_label"), action="store", dest="short_label", help="Hub short label"),
- 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_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);
+create_primary_html = function(output_trackhub, hub_dir) {
+ hub_dir_files <- list.files(path=hub_dir);
s <- paste('', sep="\n");
- s <- paste(s, 'Contents of directory ~/myHub/', build, ' required by UCSC TrackHub
\n', sep="");
+ s <- paste(s, 'Contents of directory ~/myHub', ' 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="");
+ for (i in 1:length(hub_dir_files)) {
+ s <- paste(s, '- ', hub_dir_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_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);
@@ -99,8 +102,8 @@
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, short_label, long_label, state_indexes, state_colors) {
+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, state_indexes, state_names, state_colors) {
# Create a trackDb.txt file that includes each state.
para_files <- list.files(path=input_dir_para, full.names=TRUE);
######
@@ -108,10 +111,8 @@
# are multiple .para files. See the comments in the for loop
# below.
data_frame <- read.table(para_files[1], comment="!", header=T);
- color_hex_code <- create_heatmap(data_frame);
+ color_hex_code <- create_heatmap(data_frame);
######
- base_track_file_name <- paste(tracks_dir, hub_name, sep="");
- cells = create_track(input_dir_state, chrom_len_file, base_track_file_name);
if (!is.null(state_indexes)) {
# Split state_indexes into a list of integers.
s_indexes <- c();
@@ -120,6 +121,19 @@
for (item in items) {
s_indexes <- c(s_indexes, as.integer(item));
}
+ # Split state_names into a list of strings.
+ s_names <- c();
+ name_str <- as.character(state_colors);
+ items <- strsplit(name_str, ",");
+ item_index <- 0;
+ for (item in items) {
+ item_index = item_index + 1;
+ # Handle the special string "use state index".
+ if (identical(item, "use state index")) {
+ item <- s_indexes[item_index];
+ }
+ s_names <- c(s_names, item);
+ }
# Split state_colors into a list of strings.
s_colors <- c();
color_str <- as.character(state_colors);
@@ -128,6 +142,8 @@
s_colors <- c(s_colors, item);
}
}
+ base_track_file_name <- paste(tracks_dir, hub_name, sep="");
+ cells = create_cells(input_dir_state, chrom_len_file, base_track_file_name, s_indexes, s_names, s_colors);
track_db = NULL;
for (i in 1:length(cells)) {
# Get the color for the current state.
@@ -147,8 +163,8 @@
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("shortLabel", hub_short_label, sep=" "));
+ track_db = c(track_db, paste("longLabel", hub_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");
@@ -172,11 +188,11 @@
# Create the hub.txt output.
hub_name_line <- paste("hub ", opt$hub_name, sep="");
-short_label_line <- paste("shortLabel ", opt$short_label, sep="");
-long_label_line <- paste("longLabel ", opt$long_label, 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$email, sep="");
-contents <- paste(hub_name_line, short_label_line, long_label_line, genomes_txt_line, email_line, sep="\n");
+contents <- paste(hub_name_line, hub_short_label_line, hub_long_label_line, genomes_txt_line, email_line, sep="\n");
hub_dir <- paste(opt$output_trackhub_files_path, "/", "myHub", "/", sep="");
dir.create(hub_dir, showWarnings=FALSE);
hub_file_path <- paste(hub_dir, "hub.txt", sep="");
@@ -195,12 +211,12 @@
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$short_label, opt$long_label, opt$state_indexes, opt$state_colors);
+ 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$build);
-
+create_primary_html(opt$output_trackhub, hub_dir);