fix UniProtKB DbXrefs #69

oschwengers · Aug 13, 2021 · fc4c74c · fc4c74c
1 parent 245558e
commit fc4c74c
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Showing 4 changed files with 6 additions and 10 deletions.
diff --git a/bakta/constants.py b/bakta/constants.py
@@ -18,10 +18,6 @@
 ############################################################################
 # DB identifiers
 ############################################################################
-DB_XREF_UNIREF_100 = 'UniRef100'
-DB_XREF_UNIREF_90 = 'UniRef90'
-DB_XREF_UNIREF_50 = 'UniRef50'
-DB_XREF_UNIPARC = 'UniParc'
 DB_XREF_UNIPROTKB = 'UniProtKB'
 DB_XREF_REFSEQ_NRP = 'RefSeq'
 DB_XREF_EC = 'EC'

diff --git a/bakta/ips.py b/bakta/ips.py
@@ -74,7 +74,7 @@ def parse_annotation(rec):
     }
     db_xrefs = [
         'SO:0001217',
-        f'{bc.DB_XREF_UNIREF_100}:{ips[DB_IPS_COL_UNIREF100]}'
+        f'{bc.DB_XREF_UNIPROTKB}:{ips[DB_IPS_COL_UNIREF100]}'
     ]
 
     # add non-empty PSC annotations and attach database prefixes to identifiers
@@ -84,7 +84,7 @@ def parse_annotation(rec):
         ips[DB_IPS_COL_PRODUCT] = rec[DB_IPS_COL_PRODUCT]
     if(rec[DB_IPS_COL_UNIREF90]):
         ips[DB_IPS_COL_UNIREF90] = bc.DB_PREFIX_UNIREF_90 + rec[DB_IPS_COL_UNIREF90]
-        db_xrefs.append(f'{bc.DB_XREF_UNIREF_90}:{ips[DB_IPS_COL_UNIREF90]}')
+        db_xrefs.append(f'{bc.DB_XREF_UNIPROTKB}:{ips[DB_IPS_COL_UNIREF90]}')
     if(rec[DB_IPS_COL_EC]):
         ips[DB_IPS_COL_EC] = rec[DB_IPS_COL_EC]
         ecs = []

diff --git a/bakta/psc.py b/bakta/psc.py
@@ -144,7 +144,7 @@ def parse_annotation(rec):
     }
     db_xrefs = [
         'SO:0001217',
-        f'{bc.DB_XREF_UNIREF_90}:{psc[DB_PSC_COL_UNIREF90]}'
+        f'{bc.DB_XREF_UNIPROTKB}:{psc[DB_PSC_COL_UNIREF90]}'
     ]
 
     # add non-empty PSC annotations and attach database prefixes to identifiers
@@ -162,7 +162,7 @@ def parse_annotation(rec):
             psc[DB_PSC_COL_EC] = ecs
     if(rec[DB_PSC_COL_UNIREF50]):
         psc[DB_PSC_COL_UNIREF50] = bc.DB_PREFIX_UNIREF_50 + rec[DB_PSC_COL_UNIREF50]
-        db_xrefs.append(f'{bc.DB_XREF_UNIREF_50}:{psc[DB_PSC_COL_UNIREF50]}')
+        db_xrefs.append(f'{bc.DB_XREF_UNIPROTKB}:{psc[DB_PSC_COL_UNIREF50]}')
     if(rec[DB_PSC_COL_COG_ID]):
         psc[DB_PSC_COL_COG_ID] = bc.DB_PREFIX_COG + rec[DB_PSC_COL_COG_ID]
         db_xrefs.append(f'{bc.DB_XREF_COG}:{psc[DB_PSC_COL_COG_ID]}')

diff --git a/bakta/ups.py b/bakta/ups.py
@@ -70,13 +70,13 @@ def parse_annotation(rec):
     # add non-empty PSC annotations and attach database prefixes to identifiers
     if(rec[DB_UPS_COL_UNIPARC]):
         ups[DB_UPS_COL_UNIPARC] = bc.DB_PREFIX_UNIPARC + rec[DB_UPS_COL_UNIPARC]
-        db_xrefs.append(f'{bc.DB_XREF_UNIPARC}:{ups[DB_UPS_COL_UNIPARC]}')
+        db_xrefs.append(f'{bc.DB_XREF_UNIPROTKB}:{ups[DB_UPS_COL_UNIPARC]}')
     if(rec[DB_UPS_COL_REFSEQ_NRP]):
         ups[DB_UPS_COL_REFSEQ_NRP] = bc.DB_PREFIX_REFSEQ_NRP + rec[DB_UPS_COL_REFSEQ_NRP]
         db_xrefs.append(f'{bc.DB_XREF_REFSEQ_NRP}:{ups[DB_UPS_COL_REFSEQ_NRP]}')
     if(rec[DB_UPS_COL_UNIREF100]):
         ups[DB_UPS_COL_UNIREF100] = bc.DB_PREFIX_UNIREF_100 + rec[DB_UPS_COL_UNIREF100]
-        db_xrefs.append(f'{bc.DB_XREF_UNIREF_100}:{ups[DB_UPS_COL_UNIREF100]}')
+        db_xrefs.append(f'{bc.DB_XREF_UNIPROTKB}:{ups[DB_UPS_COL_UNIREF100]}')
 
     ups['db_xrefs'] = db_xrefs
     return ups