Mercurial > repos > greg > create_genome_tracks

changeset 4:47f6ba0fc3f4 draft

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Uploaded
author greg
date Fri, 10 Nov 2017 13:55:04 -0500
parents 3bc9d3e88e7b
children a149688bd1bb
files create_genome_tracks.R
diffstat 1 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/create_genome_tracks.R	Fri Nov 10 13:50:32 2017 -0500
+++ b/create_genome_tracks.R	Fri Nov 10 13:55:04 2017 -0500
@@ -118,7 +118,7 @@
 }
 
 # Create the tracks output directory.
-tracks_output_dir = paste("tracks_", hub_id, "/", sep="");
+tracks_output_dir = paste("tracks_", opt$hub_id, "/", sep="");
 dir.create(tracks_output_dir, showWarnings=FALSE);
 
 # Create the color scheme.
@@ -137,7 +137,7 @@
 state_color = get_state_color(m, mc);
 
 # Create the tracks.
-cells = create_track(opt$state_files, opt$chrom_len_file, paste(tracks_output_dir, hub_id, sep=""), state_color, header=opt$header, state_name=opt$state_name);
+cells = create_track(opt$state_files, opt$chrom_len_file, paste(tracks_output_dir, opt$hub_id, sep=""), state_color, header=opt$header, state_name=opt$state_name);
 cell_info = opt$cell_info
 if(length(cell_info) == 0) {
     cell_info = cbind(cells, cells, cells, "#000000");
@@ -157,7 +157,7 @@
     track_db = c(track_db, "type bigBed 9 .");
     track_db = c(track_db, "itemRgb on");
     track_db = c(track_db, "maxItems 100000");
-    track_db = c(track_db, paste("bigDataUrl ", opt$target_url, hub_id, ".", i, ".bb", sep=""));
+    track_db = c(track_db, paste("bigDataUrl ", opt$target_url, opt$hub_id, ".", i, ".bb", sep=""));
     track_db = c(track_db, paste("shortLabel", cell_info[ii, 2]));
     track_db = c(track_db, paste("longLabel", paste(opt$hub_name, cell_info[ii, 3])));
     track_db = c(track_db, paste("color", paste(c(col2rgb(cell_info[ii, 4])), collapse=",")));
@@ -167,5 +167,5 @@
 
 # Write the outputs.
 write.table(track_db, opt$output_track_db, quote=F, row.names=F, col.names=F);
-write.table(c(paste("genome", opt$build), opt$output_build, paste(tracks_output_dir, "genomes_", hub_id, ".txt", sep=""), quote=F,row.names=F,col.names=F);
-write.table(c(paste("hub", hub_id), paste("shortLabel", hub_id), paste("longLabel", opt$hub_name), paste("genomesFile genomes_", hub_id, ".txt", sep=""), "email yzz2 at psu.edu"), opt$output_hub, quote=F, row.names=F, col.names=F);
+write.table(c(paste("genome", opt$build), opt$output_build, paste(tracks_output_dir, "genomes_", opt$hub_id, ".txt", sep=""), quote=F,row.names=F,col.names=F);
+write.table(c(paste("hub", opt$hub_id), paste("shortLabel", opt$hub_id), paste("longLabel", opt$hub_name), paste("genomesFile genomes_", opt$hub_id, ".txt", sep=""), "email yzz2 at psu.edu"), opt$output_hub, quote=F, row.names=F, col.names=F);