# HG changeset patch
# User trinity_ctat
# Date 1529684642 14400
# Node ID ca57480062d10b6a26bb8100bdcf5ed590cb55a3
# Parent  4cdc1ccaae76e09d9d5b611c51596e126757057f
Uploaded

diff -r 4cdc1ccaae76 -r ca57480062d1 data_manager/add_ctat_lncrna_annotations.py
--- a/data_manager/add_ctat_lncrna_annotations.py	Thu Jun 21 19:08:52 2018 -0400
+++ b/data_manager/add_ctat_lncrna_annotations.py	Fri Jun 22 12:24:02 2018 -0400
@@ -13,7 +13,7 @@
 from datetime import *
 
 # Remove the following line when testing without galaxy package:
-from galaxy.util.json import to_json_string
+# from galaxy.util.json import to_json_string
 # Am not using the following:
 # from galaxy.util.json import from_json_string
 
@@ -314,10 +314,23 @@
 
     # Temporarily the output file's dictionary is written for debugging:
     print "The dictionary for the output file is:\n\t{:s}".format(str(data_manager_dict))
+
+    # Make a new annotations.config with absolute paths
+    annot_abs_path=[]
+    with open(os.path.join(annotations_directory,"annotations.config"),"r") as annot_reader:
+        for line in annot_reader:
+            if line.startswith("ORTHOLOG="):
+                annot_abs_path.append(line)
+            else:
+                annot_abs_path.append(line.replace("=","="+annotations_directory+os.sep))
+    with open(os.path.join(annotations_directory,"annotations_abs_paths.config"),"w") as annot_writer:
+        for line in annot_abs_path:
+            annot_writer.write(line)
+
     # Save info to json file. This is used to transfer data from the DataManager tool, to the data manager,
     # which then puts it into the correct .loc file (I think).
     # Remove the following line when testing without galaxy package.
-    open(args.output_filename, 'wb').write(to_json_string(data_manager_dict))
+    # open(args.output_filename, 'wb').write(to_json_string(data_manager_dict))
 
 if __name__ == "__main__":
     main()