Adding 'pfam' nodes

PathwayMerger · Oct 5, 2018 · 6824d83 · 6824d83
1 parent 1eaa63d
commit 6824d83
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Showing 2 changed files with 10 additions and 1 deletion.
diff --git a/src/pathme/constants.py b/src/pathme/constants.py
@@ -40,6 +40,8 @@ def ensure_pathme_folders():
 
 KEGG = 'kegg'
 INTERPRO = 'interpro'
+PFAM = 'pfam'
+
 REACTOME = 'reactome'
 WIKIPATHWAYS = 'wikipathways'
 

diff --git a/src/pathme/wikipathways/utils.py b/src/pathme/wikipathways/utils.py
@@ -10,7 +10,7 @@
 import networkx as nx
 from bio2bel_wikipathways import Manager as WikiPathwaysManager
 
-from ..constants import DATA_DIR, ENSEMBL, ENTREZ, EXPASY, HGNC, KEGG, UNIPROT, WIKIPATHWAYS, WIKIPEDIA, INTERPRO
+from ..constants import DATA_DIR, ENSEMBL, ENTREZ, EXPASY, HGNC, KEGG, UNIPROT, WIKIPATHWAYS, WIKIPEDIA, INTERPRO, PFAM
 from ..utils import get_files_in_folder, check_multiple
 
 WIKIPATHWAYS_DIR = os.path.join(DATA_DIR, WIKIPATHWAYS)
@@ -153,6 +153,13 @@ def get_valid_gene_identifier(node_ids_dict, hgnc_manager):
 
         return INTERPRO, interpro_name, interpro_id
 
+    elif PFAM.lower() in node_ids_dict['uri_id']:
+        pfam_id = check_multiple(node_ids_dict['identifier'], 'pfam_id')
+        pfam_name = check_multiple(node_ids_dict['name'], 'pfam_name')
+        log.warning('Adding PFAM node %s ', pfam_id)
+
+        return PFAM, pfam_name, pfam_id
+
     raise Exception('Unknown identifier for node %s', node_ids_dict)