Mercurial > repos > greg > ideas_genome_tracks

changeset 54:d7ab58fe039f draft

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Uploaded
author greg
date Fri, 15 Dec 2017 13:41:32 -0500
parents 8b1c49f2ecaa
children 9b7405976dfe
files ideas_genome_tracks.R
diffstat 1 files changed, 114 insertions(+), 114 deletions(-) [+]
line wrap: on
line diff
--- 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('<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);
+    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_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);