Mercurial > repos > greg > ideas_genome_tracks

changeset 56:c54ef43eaee3 draft

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Uploaded
author greg
date Fri, 15 Dec 2017 16:45:01 -0500
parents 9b7405976dfe
children 7a7d5c3c5480
files ideas_genome_tracks.R
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/ideas_genome_tracks.R	Fri Dec 15 13:55:43 2017 -0500
+++ b/ideas_genome_tracks.R	Fri Dec 15 16:45:01 2017 -0500
@@ -82,7 +82,7 @@
         t = c(t, L);
         np = cbind(chr[t], posst[t0], posed[t], tstate[t]);
         track_file_name_bed <- get_track_file_name(base_track_file_name, i, "bed");
-        track_file_name_bigbed <- get_track_file_name(base_track_file_name, i, "bb");
+        track_file_name_bigbed <- get_track_file_name(base_track_file_name, i, "bigbed");
         x = cbind(np[, 1:3], state_name[as.integer(np[,4])+1], 1000, ".", np[,2:3]);
         write.table(as.matrix(x), track_file_name_bed, quote=F, row.names=F, col.names=F);
         system(paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed));
@@ -129,7 +129,7 @@
 }
 
 get_big_data_url = function(galaxy_url, encoded_dataset_id, tracks_dir, index, build) {
-    track_files <- list.files(path=tracks_dir, pattern="\\.bb");
+    track_files <- list.files(path=tracks_dir, pattern="\\.bigbed");
     s <- paste(galaxy_url, 'datasets/', encoded_dataset_id, '/display/myHub/', build, '/', track_files[index], sep="");
     return(s)
 }