Mercurial > repos > greg > create_genome_tracks

comparison create_genome_tracks.R @ 4:47f6ba0fc3f4 draft

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author greg
date Fri, 10 Nov 2017 13:55:04 -0500
parents 3bc9d3e88e7b
children d46bbaa386de
comparison
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3:3bc9d3e88e7b 4:47f6ba0fc3f4
116 if(length(opt$hub_name) == 0) { 116 if(length(opt$hub_name) == 0) {
117 hub_name = opt$hub_id; 117 hub_name = opt$hub_id;
118 } 118 }
119 119
120 # Create the tracks output directory. 120 # Create the tracks output directory.
121 tracks_output_dir = paste("tracks_", hub_id, "/", sep=""); 121 tracks_output_dir = paste("tracks_", opt$hub_id, "/", sep="");
122 dir.create(tracks_output_dir, showWarnings=FALSE); 122 dir.create(tracks_output_dir, showWarnings=FALSE);
123 123
124 # Create the color scheme. 124 # Create the color scheme.
125 mc = NULL; 125 mc = NULL;
126 x = read.table(opt$parameter_files, comment="!", nrows=1); 126 x = read.table(opt$parameter_files, comment="!", nrows=1);
135 p = x[,1] / sum(x[,1]); 135 p = x[,1] / sum(x[,1]);
136 m = array(as.matrix(x[,1:l+1] / x[,1]), dim=c(dim(x)[1], l)); 136 m = array(as.matrix(x[,1:l+1] / x[,1]), dim=c(dim(x)[1], l));
137 state_color = get_state_color(m, mc); 137 state_color = get_state_color(m, mc);
138 138
139 # Create the tracks. 139 # Create the tracks.
140 cells = create_track(opt$state_files, opt$chrom_len_file, paste(tracks_output_dir, hub_id, sep=""), state_color, header=opt$header, state_name=opt$state_name); 140 cells = create_track(opt$state_files, opt$chrom_len_file, paste(tracks_output_dir, opt$hub_id, sep=""), state_color, header=opt$header, state_name=opt$state_name);
141 cell_info = opt$cell_info 141 cell_info = opt$cell_info
142 if(length(cell_info) == 0) { 142 if(length(cell_info) == 0) {
143 cell_info = cbind(cells, cells, cells, "#000000"); 143 cell_info = cbind(cells, cells, cells, "#000000");
144 cell_info = array(cell_info, dim=c(length(cells), 4)); 144 cell_info = array(cell_info, dim=c(length(cells), 4));
145 } 145 }
155 track_db = c(track_db, paste("track bigBed", i, sep="")); 155 track_db = c(track_db, paste("track bigBed", i, sep=""));
156 track_db = c(track_db, paste("priority", ii)); 156 track_db = c(track_db, paste("priority", ii));
157 track_db = c(track_db, "type bigBed 9 ."); 157 track_db = c(track_db, "type bigBed 9 .");
158 track_db = c(track_db, "itemRgb on"); 158 track_db = c(track_db, "itemRgb on");
159 track_db = c(track_db, "maxItems 100000"); 159 track_db = c(track_db, "maxItems 100000");
160 track_db = c(track_db, paste("bigDataUrl ", opt$target_url, hub_id, ".", i, ".bb", sep="")); 160 track_db = c(track_db, paste("bigDataUrl ", opt$target_url, opt$hub_id, ".", i, ".bb", sep=""));
161 track_db = c(track_db, paste("shortLabel", cell_info[ii, 2])); 161 track_db = c(track_db, paste("shortLabel", cell_info[ii, 2]));
162 track_db = c(track_db, paste("longLabel", paste(opt$hub_name, cell_info[ii, 3]))); 162 track_db = c(track_db, paste("longLabel", paste(opt$hub_name, cell_info[ii, 3])));
163 track_db = c(track_db, paste("color", paste(c(col2rgb(cell_info[ii, 4])), collapse=","))); 163 track_db = c(track_db, paste("color", paste(c(col2rgb(cell_info[ii, 4])), collapse=",")));
164 track_db = c(track_db, "visibility dense"); 164 track_db = c(track_db, "visibility dense");
165 track_db = c(track_db, ""); 165 track_db = c(track_db, "");
166 } 166 }
167 167
168 # Write the outputs. 168 # Write the outputs.
169 write.table(track_db, opt$output_track_db, quote=F, row.names=F, col.names=F); 169 write.table(track_db, opt$output_track_db, quote=F, row.names=F, col.names=F);
170 write.table(c(paste("genome", opt$build), opt$output_build, paste(tracks_output_dir, "genomes_", hub_id, ".txt", sep=""), quote=F,row.names=F,col.names=F); 170 write.table(c(paste("genome", opt$build), opt$output_build, paste(tracks_output_dir, "genomes_", opt$hub_id, ".txt", sep=""), quote=F,row.names=F,col.names=F);
171 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); 171 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);