fixed reference identification message and added i2t.ctab and e2t.cta…

…b as outputs of stringtie

tools/StringTie

@@ -45,4 +45,7 @@ python ST_ttab_parse.py t_data.ctab > $BASE_NAME-merged_counts.fpkm
 mv t_data.ctab $BASE_NAME-t_data.ctab
 mv e_data.ctab $BASE_NAME-e_data.ctab
 mv i_data.ctab $BASE_NAME-i_data.ctab
+mv i2t.ctab $BASE_NAME-i2t.ctab
+mv e2t.ctab $BASE_NAME-e2t.ctab
+
 

tools/dax-level-1

@@ -52,18 +52,30 @@ if conf.getboolean("config", "stringtie") and conf.getboolean("config", "cufflin
 print("\nAdding reference files ...")
 count = 0
 
-for fname in os.listdir(base_dir + "/reference/star_index/"):
-#    if re.search("^" + conf.get("reference", "reference_prefix"), fname):
-#        print("    " + fname)
-#        count += 1
-#    if re.search("^" + conf.get("reference","reference_path"), fname):
+if conf.getboolean("config", "star"):
+
+    for fname in os.listdir(base_dir + "/reference/star_index/"):
 	print("    " + fname)
 	count += 1
 
-if count == 0:
-    print("ERROR: Unable to find reference files in the reference/ directory" +
-          " with the specified prefix: " + conf.get("reference", "reference_prefix"))
-    sys.exit(1)
+
+    if count == 0:
+        print("ERROR: Unable to find reference files in the reference/star_index directory" +
+              " with the specified prefix: " + conf.get("reference", "reference_prefix"))
+        sys.exit(1)
+
+
+else:
+    print("\nAdding reference files ...")
+    count = 0
+    for fname in os.listdir(base_dir + "/reference/"):
+        if re.search("^" + conf.get("reference", "reference_prefix"), fname):
+            print("    " + fname)
+            count += 1
+    if count == 0:
+        print("ERROR: Unable to find reference files in the reference/ directory" +
+              " with the specified prefix: " + conf.get("reference", "reference_prefix"))
+        sys.exit(1)
 
 print("\nAdding gff3 file ...")
 count = 0

tools/dax-level-2

@@ -353,10 +353,14 @@ def stringtie(task_files, dax, base_name, merged):
     t = File(base_name + "-t_data.ctab")
     e = File(base_name + "-e_data.ctab")
     i = File(base_name + "-i_data.ctab")
+    x = File(base_name + "-i2t.ctab")
+    z = File(base_name + "-e2t.ctab")
     j.uses(e, link=Link.OUTPUT, transfer=True)
     j.uses(i, link=Link.OUTPUT, transfer=True)
     j.uses(f, link=Link.OUTPUT, transfer=True)
     j.uses(t, link=Link.OUTPUT, transfer=True)
+    j.uses(x, link=Link.OUTPUT, transfer=True)
+    j.uses(z, link=Link.OUTPUT, transfer=True)
     dax.addJob(j)
 
     return f