changeset 96:cef03f812888 draft

Uploaded

--- a/ideas_genome_tracks.R	Thu Feb 15 11:06:05 2018 -0500
+++ b/ideas_genome_tracks.R	Fri Feb 16 09:18:06 2018 -0500
@@ -86,7 +86,7 @@
         t0 = c(0, t) + 1;
         t = c(t, L);
         np = cbind(chr[t], posst[t0], posed[t], tstate[t]);
-        x = cbind(np[, 1:3], state_names[as.integer(np[,4])+1], 1000, ".", np[,2:3], color_codes_vector[as.numeric(np[,4])+1]);
+        x = cbind(np[,1:3], state_names[as.integer(np[,4])+1], 1000, ".", np[,2:3], color_codes_vector[as.numeric(np[,4])+1]);
         track_file_name_bed_unsorted <- get_track_file_name(base_track_file_name, i, "bed_unsorted");
         track_file_name_bed <- get_track_file_name(base_track_file_name, i, "bed");
         write.table(as.matrix(x), track_file_name_bed_unsorted, quote=F, row.names=F, col.names=F);
@@ -108,11 +108,17 @@
     color_codes_vectors_by_para_file = list();
     # IDEAS state indexes are zero based.
     index = 0;
-    para_files = list.files(path=input_dir_para, full.names=TRUE);
-    # Generate the default state names and colors.
-    for (para_file in para_files) {
+    state_files = list.files(path=input_dir_state, full.names=TRUE);
+    # Generate the default state names.
+    for (state_file in state_files) {
         # Append the default state name.
         state_names = c(state_names, toString(index));
+        index = index + 1;
+    }
+    # Generate the default colors.
+    index = 0;
+    para_files = list.files(path=input_dir_para, full.names=TRUE);
+    for (para_file in para_files) {
         # Append the default color codes vector.
         data_frame = read.table(para_file, comment="!", header=T);
         # Here state_color_codes_vector contains an rgb
@@ -185,7 +191,7 @@
             }
         }
     } else {
-        color_codes_vector = color_codes_vectors_by_para_file[1];
+        color_codes_vector = color_codes_vectors_by_para_file[[1]];
     }
     # Create the bigbed track files.
     create_tracks(input_dir_state, chrom_len_file, base_track_file_name, state_names, color_codes_vector);
@@ -287,4 +293,4 @@
 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$output_trackhub, trackhub_dir);
+create_primary_html(opt$output_trackhub, trackhub_dir);
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