working version of implanting annotations

map_generator/utils/implant_annotations.py

@@ -2,11 +2,10 @@ import logging
 import argparse
 import pandas as pd
 import xml.etree.ElementTree as ET
-from . import utils
-
-
-
+import utils
 
+def get_full_name(elem_name, ns, nss) -> str:
+    return "{{{}}}{}".format(nss[ns], elem_name)
 
 def implant(map_path: str, variants_path: str) -> str:
 
@@ -15,22 +14,21 @@ def implant(map_path: str, variants_path: str) -> str:
     for name, g in df_vars.groupby('gene_name')['identifier_uniprot']:
         gene_uniprot[name] = set(g)
 
-    utils.register_namespaces(map_path)
+    namespaces = utils.register_namespaces(map_path)
     tree = ET.parse(map_path)
     root = tree.getroot()
 
-    for elem in root.iter('species'):
-        atts = elem.attrib
-        # if 'name' in atts:
-        #     print(elem.tag, atts)
-        for k, v in atts.items():
-            if len(v) > 250:
-                logging.warning("Trimming {} (key {} too long)".format(elem, k))
-                if "resource" in k:
-                    #  We want to keep the RDF resource still a valid resource otherwise MINERVA will fail during import
-                    atts[k] = atts[k].split(";")[0]
-                else:
-                    atts[k] = ""
+    for elem in list(root.iter(get_full_name("species", "", namespaces))):
+    # for elem in root.iterfind(get_full_name("layout", "layout", namespaces)):
+        name = elem.attrib["name"]
+        if name in gene_uniprot:
+            for uniprot_id in gene_uniprot[name]:
+                idb = ET.Element('bqbiol:isDescribedBy')
+                b = ET.SubElement(idb, 'rdf:Bag')
+                urn_key = 'urn:miriam:uniprot' if '-' not in uniprot_id else 'urn:miriam:uniprot.isoform'
+                ET.SubElement(b, 'rdf:li', {'rdf:resource': "{}:{}".format(urn_key, uniprot_id)})
+                elem.append(idb)
+
 
     return ET.tostring(root, encoding='utf8').decode('utf8')
 

map_generator/utils/utils.py

 import xml.etree.ElementTree as ET
 import re
+from typing import Dict
 
-def register_namespaces(path):
+def register_namespaces(path) -> Dict:
+    namespaces = {}
     with open(path) as f:
         content = f.read()
         sbml_tag = re.search(r'<sbml([^>]*)>', content).group(1)
         for ns in re.finditer(r'xmlns:*([^=]*)="([^"]*)"', sbml_tag ):
-            ET.register_namespace(ns.group(1), ns.group(2))
\ No newline at end of file
+            k = ns.group(1)
+            v = ns.group(2)
+            # if not name:
+            #     name = "core"
+            ET.register_namespace(k, v)
+            namespaces[k] = v
+    return namespaces
\ No newline at end of file