# HG changeset patch
# User trinity_ctat
# Date 1529603940 14400
# Node ID 1456dba605b8e72594fc67e5522ab1f3c08fef17
# Parent  7a1a78b8079b60172ca725ff585b9664fbf80fba
Uploaded

diff -r 7a1a78b8079b -r 1456dba605b8 data_manager/add_ctat_lncrna_annotations.py
--- a/data_manager/add_ctat_lncrna_annotations.py	Thu Jun 21 13:40:54 2018 -0400
+++ b/data_manager/add_ctat_lncrna_annotations.py	Thu Jun 21 13:59:00 2018 -0400
@@ -245,15 +245,16 @@
     print "\nThe location of the Lncrna annotations is {:s}.\n".format(annotations_directory)
     files_in_annotations_directory = set(os.listdir(annotations_directory))
     annotations_file_found = False
-    annotations_file_path_mm9 = annotations_directory+"/mm9"
-    annotations_file_path_mm10 = annotations_directory+"/mm10"
-    annotations_file_path_hg19 = annotations_directory+"/hg19"
-    annotations_file_path_hg38 = annotations_directory+"/hg38"
+    annotations_file_path_mm9 = annotations_directory #+"/mm9"
+    annotations_file_path_mm10 = annotations_directory #+"/mm10"
+    annotations_file_path_hg19 = annotations_directory #+"/hg19"
+    annotations_file_path_hg38 = annotations_directory #+"/hg38"
 
     # Set the display_name
     # if (args.display_name is None) or (args.display_name == ""):
         # Use the root_annotations_dirname.
         # print "display_name_ok$$$$$$$"
+    
     if (root_annotations_dirname != None) and (root_annotations_dirname != ""):
         print "root_annotations_ok%%%%"
         display_name_hg19 = "hg19"
@@ -299,16 +300,16 @@
     data_manager_dict = {}
     data_manager_dict['data_tables'] = {}
     data_manager_dict['data_tables'][_CTAT_lncrnaTableName] = []
-    data_table_entry_mm9 = dict(value=mm9_unique_id, name=display_name_mm9, path=annotations_file_path_mm9)
+    data_table_entry_mm9 = dict(value=display_name_mm9, name=display_name_mm9, path=annotations_file_path_mm9)
     data_manager_dict['data_tables'][_CTAT_lncrnaTableName].append(data_table_entry_mm9)
 
-    data_table_entry_mm10 = dict(value=mm10_unique_id, name=display_name_mm10, path=annotations_file_path_mm10)
+    data_table_entry_mm10 = dict(value=display_name_mm10, name=display_name_mm10, path=annotations_file_path_mm10)
     data_manager_dict['data_tables'][_CTAT_lncrnaTableName].append(data_table_entry_mm10)
 
-    data_table_entry_hg19 = dict(value=hg19_unique_id, name=display_name_hg19, path=annotations_file_path_hg19)
+    data_table_entry_hg19 = dict(value=display_name_hg19, name=display_name_hg19, path=annotations_file_path_hg19)
     data_manager_dict['data_tables'][_CTAT_lncrnaTableName].append(data_table_entry_hg19)
 
-    data_table_entry_hg38 = dict(value=hg38_unique_id, name=display_name_hg38, path=annotations_file_path_hg38)
+    data_table_entry_hg38 = dict(value=display_name_hg38, name=display_name_hg38, path=annotations_file_path_hg38)
     data_manager_dict['data_tables'][_CTAT_lncrnaTableName].append(data_table_entry_hg38)
 
     # Temporarily the output file's dictionary is written for debugging: