Mercurial > repos > greg > ideas_genome_tracks

changeset 33:65c6fc10465b draft

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Uploaded
author greg
date Fri, 08 Dec 2017 14:13:04 -0500
parents 38036d966bf2
children 39a6a32c3dc3
files ideas_genome_tracks.R
diffstat 1 files changed, 13 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/ideas_genome_tracks.R	Mon Nov 27 11:48:28 2017 -0500
+++ b/ideas_genome_tracks.R	Fri Dec 08 14:13:04 2017 -0500
@@ -59,7 +59,7 @@
     return(track_file_name);
 }
 
-get_track_color = function(statemean, markcolor=NULL) {   
+get_track_color = function(statemean, markcolor=NULL) {
     sm_width = dim(statemean)[1];
     sm_height = dim(statemean)[2];
     if (length(markcolor) == 0) {
@@ -90,8 +90,7 @@
     track_files <- list.files(path=tracks_dir);
     s <- paste('<html>\n    <head>\n    </head>\n    <body>\n        <ul>\n', sep="");
         for (i in 1:length(track_files)) {
-            track_file <- paste("tracks", track_files[i], sep="/");
-            s <- paste(s, '            <li><a href="', track_file, '">', track_file, '</a></li>\n', sep="");
+            s <- paste(s, '            <li><a href="', track_files[i], '">', track_files[i], '</a></li>\n', sep="");
         }
     s <- paste(s, '        </ul>\n    </body>\n</html>', sep="");
     cat(s, file=output_trackhub);
@@ -106,7 +105,7 @@
         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,];
         }
@@ -178,7 +177,7 @@
         track_db = c(track_db, "maxItems 100000");
         track_db = c(track_db, paste("color", paste(c(col2rgb(cell_info[ii,4])), collapse=","), sep=" "));
         track_db = c(track_db, "visibility dense");
-        track_db = c(track_db, ""); 
+        track_db = c(track_db, "");
     }
     return(track_db);
 }
@@ -191,14 +190,21 @@
 }
 
 # Create the hub.txt output.
-contents <- c(paste("hub", opt$hub_name), paste("shortLabel",opt$short_label), paste("longLabel", opt$long_label), paste("genomesFile genomes.txt", sep=""), paste("email", opt$email));
+hub_name_line <- paste("hub ", opt$hub_name, sep = "");
+short_label_line <- paste("shortLabel ", opt$short_label, sep = "");
+long_label_line <- paste("longLabel ", opt$longLabel, sep = "");
+genomes_txt_line <- paste("genomesFile genomes.txt", sep="");
+email_line <- paste("email ", opt$email, sep = "");
+contents <- c(paste(hub_name_line, short_label_line, long_label_line, genomes_txt_line, email_line), sep="");
 hub_dir <- paste(opt$output_trackhub_files_path, "/", "myHub", "/", sep="");
 dir.create(hub_dir, showWarnings=FALSE);
 hub_file_path <- paste(hub_dir, "hub.txt", sep="");
 write.table(contents, file=hub_file_path, quote=F, row.names=F, col.names=F);
 
 # Create the genomes.txt output.
-contents <- c(paste("genome", opt$build), paste("trackDb ", opt$build, "/", "trackDb.txt", sep=""));
+genome_line <- paste("genome", opt$build, sep="");
+track_db_line <- paste("trackDb ", opt$build, "/", "trackDb.txt", sep="");
+contents <- c(paste(genome_line, track_db_line), sep="");
 genomes_file_path <- paste(hub_dir, "genomes.txt", sep="");
 write.table(contents, file=genomes_file_path, quote=F, row.names=F, col.names=F);