Mercurial > repos > greg > ideas_genome_tracks

changeset 57:7a7d5c3c5480 draft

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Uploaded
author greg
date Sat, 16 Dec 2017 13:11:47 -0500
parents c54ef43eaee3
children 269241d4b9c8
files ideas_genome_tracks.R
diffstat 1 files changed, 6 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/ideas_genome_tracks.R	Fri Dec 15 16:45:01 2017 -0500
+++ b/ideas_genome_tracks.R	Sat Dec 16 13:11:47 2017 -0500
@@ -81,12 +81,15 @@
         t0 = c(0, t) + 1;
         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_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");
         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);
+        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"), sep=" ");
         system(paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed));
-        system(paste("rm ", track_file_name_bed));
+		system(paste("rm ", track_file_name_bed_unsorted));
+		system(paste("rm ", track_file_name_bed));
     }
     return(cells);
 }