Restructure static to consolidate gene ID mapping files

bioinfodlsu · Sep 8, 2023 · 983e594 · 983e594
1 parent 43db3a8
commit 983e594
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/callbacks/coexpression/util.py b/callbacks/coexpression/util.py
@@ -264,7 +264,7 @@ def convert_transcript_to_msu_id(transcript_ids_str, network):
     Returns:
     - Equivalent MSU accessions of the KEGG transcript IDs
     """
-    with open(f'{Constants.GENE_ID_MAPPING}/{network}/transcript-to-msu-id.pickle', 'rb') as f:
+    with open(f'{Constants.MSU_MAPPING}/{network}/transcript-to-msu-id.pickle', 'rb') as f:
         mapping_dict = pickle.load(f)
 
     output_str = ''

diff --git a/callbacks/constants.py b/callbacks/constants.py
@@ -11,13 +11,15 @@ class Constants(object):
 
     ANNOTATIONS = f'{APP_DATA}/annotations'
     ALIGNMENTS = f'{APP_DATA}/alignments'
-    OGI_MAPPING = f'{APP_DATA}/ogi_mapping'
-    NB_MAPPING = f'{APP_DATA}/nb_mapping'
     GENE_DESCRIPTIONS = f'{APP_DATA}/gene_descriptions'
-    GENE_ID_MAPPING = f'{APP_DATA}/gene_id_mapping'
     TEXT_MINING = f'{APP_DATA}/text_mining'
     QTARO = f'{APP_DATA}/qtaro'
 
+    GENE_ID_MAPPING = f'{APP_DATA}/gene_id_mapping'
+    MSU_MAPPING = f'{GENE_ID_MAPPING}/msu_mapping'
+    OGI_MAPPING = f'{GENE_ID_MAPPING}/ogi_mapping'
+    NB_MAPPING = f'{GENE_ID_MAPPING}/nb_mapping'
+
     GENOMES_NIPPONBARE = f'{APP_DATA}/genomes/Nipponbare'
     ANNOTATIONS_NB = f'{ANNOTATIONS}/Nb'
     OPEN_CHROMATIN = f'{APP_DATA}/open_chromatin'