Mercurial > repos > greg > ideas_genome_tracks

changeset 34:39a6a32c3dc3 draft

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Uploaded
author greg
date Fri, 08 Dec 2017 14:21:38 -0500
parents 65c6fc10465b
children 3e001c30b0f7
files ideas_genome_tracks.R
diffstat 1 files changed, 11 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/ideas_genome_tracks.R	Fri Dec 08 14:13:04 2017 -0500
+++ b/ideas_genome_tracks.R	Fri Dec 08 14:21:38 2017 -0500
@@ -190,31 +190,31 @@
 }
 
 # Create the hub.txt output.
-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 = "");
+hub_name_line <- c(paste("hub ", opt$hub_name), sep = "");
+short_label_line <- c(paste("shortLabel ", opt$short_label), sep = "");
+long_label_line <- c(paste("longLabel ", opt$longLabel), sep = "");
+genomes_txt_line <- c(paste("genomesFile genomes.txt"), sep="");
+email_line <- c(paste("email ", opt$email), sep = "");
 contents <- c(paste(hub_name_line, short_label_line, long_label_line, genomes_txt_line, email_line), sep="");
-hub_dir <- paste(opt$output_trackhub_files_path, "/", "myHub", "/", sep="");
+hub_dir <- c(paste(opt$output_trackhub_files_path, "/", "myHub", "/"), sep="");
 dir.create(hub_dir, showWarnings=FALSE);
-hub_file_path <- paste(hub_dir, "hub.txt", sep="");
+hub_file_path <- c(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.
-genome_line <- paste("genome", opt$build, sep="");
-track_db_line <- paste("trackDb ", opt$build, "/", "trackDb.txt", sep="");
+genome_line <- c(paste("genome", opt$build), sep="");
+track_db_line <- c(paste("trackDb ", opt$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);
 
 # Create the tracks.
-tracks_dir <- paste(hub_dir, opt$build, "/", sep="");
+tracks_dir <- c(paste(hub_dir, opt$build, "/"), sep="");
 dir.create(tracks_dir, showWarnings=FALSE);
 track_db <- create_track_db(opt$input_dir_state, opt$chrom_len_file, tracks_dir, opt$hub_name, opt$short_label, opt$long_label, track_color);
 
 # Create the trackDb.txt output.
-track_db_file_path <- paste(tracks_dir, "trackDb.txt", sep="");
+track_db_file_path <- c(paste(tracks_dir, "trackDb.txt"), sep="");
 write.table(track_db, file=track_db_file_path, quote=F, row.names=F, col.names=F);
 
 # Create the primary HTML dataset.