5fda6e8bf3df270b17862b82d875f1fd2cb3e7b7
chmalee
  Fri Apr 3 11:41:42 2020 -0700
Fixing ubuntu specific bug in expMatrixToBarchartBed, refs #25284

diff --git src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
index c66c87c..3f0f45e 100755
--- src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
+++ src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
@@ -285,32 +285,32 @@
         tpmCutoffs.append(tpmMedian[blockSizes*i])
 
     # Sort the bed like file to prepare it for the join.
     sortedBedLikeFile = tempfile.NamedTemporaryFile( mode = "w+", bufsize = 1)
     cmd = "sort -k1 " + bedLikeFile.name + " > " + sortedBedLikeFile.name
     os.system(cmd)
 
     # Sort the coordinate file to prepare it for the join.
     sortedCoords = tempfile.NamedTemporaryFile( mode = "w+", bufsize = 1)
     cmd = "sort -k4 " + options.bedFile + " > " + sortedCoords.name
     os.system(cmd)
 
     # Join the bed-like file and the coordinate file, the awk accounts for any extra
     # fields that may be included, and keeps the file in standard bed 6+5 format
     joinedFile = tempfile.NamedTemporaryFile(mode="w+", bufsize=1)
-    cmd = "join -t $'\\t' -1 4 -2 1 " + sortedCoords.name + " " + sortedBedLikeFile.name + \
-            " | awk -F'\t' -v OFS=\"\\t\" '{printf \"%s\\t%s\\t%s\\t%s\", $2,$3,$4,$1; " + \
+    cmd = "join -t '	' -1 4 -2 1 " + sortedCoords.name + " " + sortedBedLikeFile.name + \
+            " | awk -F'\\t' -v OFS=\"\\t\" '{printf \"%s\\t%s\\t%s\\t%s\", $2,$3,$4,$1; " + \
             "for (i=5;i<=NF;i++) {printf \"\\t%s\", $i}; printf\"\\n\";}' > " + joinedFile.name
     os.system(cmd)
 
     # Go through the joined file and re arrange the columns creating a bed 6+5+ file.
     # Also assign a scaled score 0 - 1000 to each tpm value.
     bedFile = tempfile.NamedTemporaryFile(mode="w+", bufsize=1)
     for line in joinedFile:
         splitLine = line.strip("\n").split("\t")
         # Drop sequences where start is greater than end.
         if (float(splitLine[1]) > float(splitLine[2])):
             sys.stderr.write("This transcript: " + splitLine[0] + " was dropped since chr end, " + \
                     splitLine[2] + ", is smaller than chr start, " + splitLine[1] + ".\n")
             continue
         score = str(determineScore(tpmCutoffs, float(splitLine[-3])))
         if autoSql: