diff --git a/bakta/constants.py b/bakta/constants.py index bf82491e..ca2ffac7 100644 --- 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 index 5ddc25af..1bf6ff00 100644 --- 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 index b310cebd..784204c5 100644 --- 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 index 4345ca25..7595fa0c 100644 --- 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