be more explicit with GO terms from interpro (untested) #959

funannotate/aux_scripts/iprscan2annotations.py

@@ -12,12 +12,12 @@
 
 def convertGOattribute(namespacein):
     namespace = namespacein.upper()
-    if namespace == 'BIOLOGICAL_PROCESS':
-        attribute = 'go_process'
-    elif namespace == 'MOLECULAR_FUNCTION':
-        attribute = 'go_function'
-    elif namespace == 'CELLULAR_COMPONENT':
-        attribute = 'go_component'
+    if namespace == "BIOLOGICAL_PROCESS":
+        attribute = "go_process"
+    elif namespace == "MOLECULAR_FUNCTION":
+        attribute = "go_function"
+    elif namespace == "CELLULAR_COMPONENT":
+        attribute = "go_component"
     else:
         # print(f'Error parsing XML GO terms: {namespace} is not a valid term')
         attribute = "go_unknown"
@@ -26,30 +26,29 @@ def convertGOattribute(namespacein):
 
 
 def main():
-    '''Main step of intepro annotations to tab delimited script.'''
+    """Main step of intepro annotations to tab delimited script."""
 
     if len(sys.argv) < 2:
         print("Usage: iprscan2annotations.py IPRSCAN.xml OUTPUT.annotations.txt")
         sys.exit(1)
 
     goDict = {}
-    for item in obo_parser.OBOReader(os.path.join(os.environ["FUNANNOTATE_DB"],
-                                                  'go.obo')):
+    for item in obo_parser.OBOReader(
+        os.path.join(os.environ["FUNANNOTATE_DB"], "go.obo")
+    ):
         namespace = convertGOattribute(item.namespace)
-        goDict[item.id] = {'name': item.name,
-                           'namespace': namespace}
+        goDict[item.id] = {"name": item.name, "namespace": namespace}
         for nm in item.alt_ids:  # also index by alt_id since that may be reported
-            goDict[nm] = {'name': item.name,
-                          'namespace': namespace}
-    with open(sys.argv[2], 'w') as output:
+            goDict[nm] = {"name": item.name, "namespace": namespace}
+    with open(sys.argv[2], "w") as output:
         with open(sys.argv[1]) as xml_file:
             tree = etree.iterparse(xml_file)
             for _, elem in tree:
-                if '}' in elem.tag:
-                    elem.tag = elem.tag.split('}', 1)[1]
+                if "}" in elem.tag:
+                    elem.tag = elem.tag.split("}", 1)[1]
                 for at in list(elem.attrib.keys()):
-                    if '}' in at:
-                        newat = at.split('}', 1)[1]
+                    if "}" in at:
+                        newat = at.split("}", 1)[1]
                         elem.attrib[newat] = elem.attrib[at]
                         del elem.attrib[at]
             root = tree.root
@@ -60,20 +59,23 @@ def main():
                 gos = {}
                 signalp = []
                 for lv1 in hits:
-                    if lv1.tag == 'xref':
-                        name = lv1.get('id')
+                    if lv1.tag == "xref":
+                        name = lv1.get("id")
                         IDs.append(name)
-                    if lv1.tag == 'matches':
-                        for e in lv1.findall('.//entry'):
-                            if not e.get('ac') in iprs:
-                                iprs.append(e.get('ac'))
-                        for g in lv1.findall('.//go-xref'):
-                            cat, goID, desc = g.get(
-                                'category'), g.get('id'), g.get('name')
-                            if cat is None or desc is None:
+                    if lv1.tag == "matches":
+                        for e in lv1.findall(".//entry"):
+                            if not e.get("ac") in iprs:
+                                iprs.append(e.get("ac"))
+                        for g in lv1.findall(".//go-xref"):
+                            cat = g.get("category", None)
+                            goID = g.get("id", None)
+                            desc = g.get("name", None)
+                            if not goID:
+                                continue
+                            if not cat or not desc:
                                 if goID in goDict:
-                                    cat = goDict[goID]['namespace']
-                                    desc = goDict[goID]['name']
+                                    cat = goDict[goID]["namespace"]
+                                    desc = goDict[goID]["name"]
                                 else:
                                     continue
                                     # cat = ""
@@ -86,23 +88,24 @@ def main():
                                 gos[goID] = goHit
                         # signalp is processed elsewhere
                         # do we just skip this parsing even?
-                        for s in lv1.findall('.//signalp-match'):
-                            for lib in s.findall('.//signature-library-release'):
-                                if lib.get('library') == "SIGNALP_EUK":
-                                    for loc in s.findall('.//signalp-location'):
+                        for s in lv1.findall(".//signalp-match"):
+                            for lib in s.findall(".//signature-library-release"):
+                                if lib.get("library") == "SIGNALP_EUK":
+                                    for loc in s.findall(".//signalp-location"):
                                         signalp.append(
-                                            (loc.get('start'), loc.get('end')))
+                                            (loc.get("start"), loc.get("end"))
+                                        )
                 # print out annotation file if IPR domains
                 if len(iprs) > 0:
                     for i in IDs:
                         for x in iprs:
-                            output.write(f'{i}\tdb_xref\tInterPro:{x}\n')
+                            output.write(f"{i}\tdb_xref\tInterPro:{x}\n")
                 if len(gos) > 0:
                     for i in IDs:
                         for goid in gos:
                             x = gos[goid]
-                            GOID = x[2].replace('GO:', '')
-                            output.write(f'{i}\t{x[0]}\t{x[1]}|{GOID}||IEA\n')
+                            GOID = x[2].replace("GO:", "")
+                            output.write(f"{i}\t{x[0]}\t{x[1]}|{GOID}||IEA\n")
 
 
 if __name__ == "__main__":