Mercurial > repos > greg > ideas_genome_tracks

changeset 61:5acfb82e4f44 draft

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Uploaded
author greg
date Tue, 19 Dec 2017 09:11:42 -0500
parents 8baf6aa848d1
children ce217f091366
files ideas_genome_tracks.R
diffstat 1 files changed, 53 insertions(+), 29 deletions(-) [+]
line wrap: on
line diff
--- a/ideas_genome_tracks.R	Tue Dec 19 09:11:35 2017 -0500
+++ b/ideas_genome_tracks.R	Tue Dec 19 09:11:42 2017 -0500
@@ -5,17 +5,19 @@
 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"),
+    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")
 )
 
 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
@@ -90,32 +92,54 @@
         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));
+        #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_state, build, chrom_len_file, tracks_dir, hub_name, short_label, long_label) {
+create_track_db = function(galaxy_url, encoded_dataset_id, input_dir_state, build, chrom_len_file, tracks_dir, hub_name, short_label, long_label, state_indexes, state_colors) {
     # 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();
+    if (is.null(state_indexes)) {
+        # 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();
+    } else {
+        # Split state_indexes into a list of integers.
+        indexes <- c();
+        index_str <- as.character(state_indexes);
+        items <- strsplit(index_str, ",")
+        for (item in items) {
+            indexes <- c(indexes, as.integer(item));
+        }
+        # Split state_colors into a list of strings.
+        colors <- c();
+        color_str <- as.character(state_colors);
+        items <- strsplit(color_str, ",");
+        for (item in items) {
+            colors <- c(colors, item);
+        }
+    }
     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)
+        if (is.null(state_indexes) || !is.element(i, indexes)) {
+            # 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.
+            color_hex_code <- viridis_vector[color_index];
+        } else {
+            # Use the selected color for the current state.
+            color_hex_code <- colors[i];
         }
-        # 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=""));
@@ -126,7 +150,7 @@
         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, paste("color", paste(c(col2rgb(color_hex_code)), collapse=","), sep=" "));
         track_db = c(track_db, "visibility dense");
         track_db = c(track_db, "");
     }
@@ -166,7 +190,7 @@
 # Create the tracks.
 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_state, opt$build, opt$chrom_len_file, tracks_dir, opt$hub_name, opt$short_label, opt$long_label);
+track_db <- create_track_db(opt$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$long_label, opt$state_indexes, opt$state_colors);
 
 # Create the trackDb.txt output.
 track_db_file_path <- paste(tracks_dir, "trackDb.txt", sep="");