fix: export all rootHOGs

Author: sinamajidian

utils/pickle2orthoxml.py

@@ -25,9 +25,12 @@
     input_pickle= sys.argv[2]   # "file_D0680685.pickle"
     handle=open(input_pickle,'rb')
     orthoxml_file = pickle.load(handle)
-
-    print(len(orthoxml_file))
-    xml_str = minidom.parseString(ET.tostring(orthoxml_file[0])).toprettyxml(indent="   ")
+    
+    print(len(orthoxml_file)) # this should be the number of rootHOGs, perhaps dup at root
+    xml_str = ""
+    for item in orthoxml_file:
+        xml_str += minidom.parseString(ET.tostring(item)).toprettyxml(indent="   ")
+        xml_str += "\n"
 
     with open(input_pickle+"_noheader.orthoxml","w") as out_file:
         out_file.write(xml_str)