Fix for either a bug or undocumented feature in ElementTree that broke megablast and blast+ XML parsing in Python 2.7.

tools/metag_tools/megablast_xml_parser.py

@@ -53,7 +53,7 @@ def __main__():
                query = elem.findtext( "Iteration_query-def" )
                qLen = elem.findtext( "Iteration_query-len" )
                # for every <Hit> within <Iteration>
-               for hit in elem.findall( "Iteration_hits/Hit/" ):
+               for hit in elem.findall( "Iteration_hits/Hit" ):
                    subject = hit.findtext( "Hit_id" )
                    if re.search( '^gi', subject ):
                        subject = subject.split('|')[1]

tools/ncbi_blast_plus/blastxml_to_tabular.py

@@ -138,7 +138,7 @@ for event, elem in context:
         qlen = int(elem.findtext("Iteration_query-len"))
                                         
         # for every <Hit> within <Iteration>
-        for hit in elem.findall("Iteration_hits/Hit/"):
+        for hit in elem.findall("Iteration_hits/Hit"):
             #Expecting either this,
             # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>
             # <Hit_def>RecName: Full=Rhodopsin</Hit_def>