Mercurial > repos > greg > ideas_genome_tracks

changeset 59:1736d09a6927 draft

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Uploaded
author greg
date Mon, 18 Dec 2017 09:09:00 -0500
parents 269241d4b9c8
children 8baf6aa848d1
files ideas_genome_tracks.R
diffstat 1 files changed, 4 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/ideas_genome_tracks.R	Mon Dec 18 07:40:15 2017 -0500
+++ b/ideas_genome_tracks.R	Mon Dec 18 09:09:00 2017 -0500
@@ -86,8 +86,10 @@
         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_unsorted, quote=F, row.names=F, col.names=F);
-        system(paste("LC_COLLATE=C sort -k1,1 -k2,2n < ", track_file_name_bed_unsorted, " > track_file_name_bed"));
-        system(paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed));
+        cmd = paste("LC_COLLATE=C sort -k1,1 -k2,2n < ", track_file_name_bed_unsorted, " > ", track_file_name_bed);
+        system(cmd);
+        cmd = paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed);
+        system(cmd);
         system(paste("rm ", track_file_name_bed_unsorted));
         system(paste("rm ", track_file_name_bed));
     }