Initial port to python3

[htsworkflow.git] / htsworkflow / pipelines / summary.py

diff --git a/htsworkflow/pipelines/summary.py b/htsworkflow/pipelines/summary.py
index 8f47670d99521f37fc8afe75ab8edf292b4c5396..c3c5919977d3f3847a981f0ed826ea6bb9d1f301 100644 (file)
--- a/htsworkflow/pipelines/summary.py
+++ b/htsworkflow/pipelines/summary.py
@@ -40,9 +40,9 @@ class Summary(object):
 
     def get_elements(self):
         summary = etree.Element(Summary.SUMMARY,
-                                      {'version': unicode(Summary.XML_VERSION)})
+                                      {'version': str(Summary.XML_VERSION)})
         for end in self.lane_results:
-            for lane in end.values():
+            for lane in list(end.values()):
                 summary.append(lane.get_elements())
         return summary
 
@@ -67,7 +67,7 @@ class Summary(object):
         Debugging function, report current object
         """
         tree = self.get_elements()
-        print etree.tostring(tree)
+        print(etree.tostring(tree))
 
 class SummaryGA(Summary):
     def __init__(self, filename=None, xml=None):
@@ -130,7 +130,7 @@ class SummaryGA(Summary):
                             ('Lane Results Summary : Read 1', 0),
                             ('Lane Results Summary : Read 2', 1),]
             for name, end in table_names:
-                if tables.has_key(name):
+                if name in tables:
                     self._extract_lane_results_for_end(tables, name, end)
 
         if len(self.lane_results[0])  == 0:
@@ -280,13 +280,13 @@ class LaneResultSummary(object):
     def get_elements(self):
         lane_result = etree.Element(
                         LaneResultSummary.LANE_RESULT_SUMMARY,
-                        {'lane': unicode(self.lane), 'end': unicode(self.end)})
-        for tag, variable_name in LaneResultSummary.TAGS.items():
+                        {'lane': str(self.lane), 'end': str(self.end)})
+        for tag, variable_name in list(LaneResultSummary.TAGS.items()):
             value = getattr(self, variable_name)
             if value is None:
                 continue
             # it looks like a sequence
-            elif type(value) in (types.TupleType, types.ListType):
+            elif type(value) in (tuple, list):
                 element = make_mean_range_element(
                   lane_result,
                   tag,
@@ -294,7 +294,7 @@ class LaneResultSummary(object):
                 )
             else:
                 element = etree.SubElement(lane_result, tag)
-                element.text = unicode(value)
+                element.text = str(value)
         return lane_result
 
     def set_elements(self, tree):
@@ -311,7 +311,7 @@ class LaneResultSummary(object):
                 variable_name = tags[element.tag]
                 setattr(self, variable_name,
                         parse_summary_element(element))
-            except KeyError, e:
+            except KeyError as e:
                 LOGGER.warn('Unrecognized tag %s' % (element.tag,))
 
 
@@ -333,7 +333,7 @@ class LaneResultSummaryGA(LaneResultSummary):
         else:
             self.lane_yield = None
 
-        for GeraldName, LRSName in LaneResultSummary.GERALD_TAGS.items():
+        for GeraldName, LRSName in list(LaneResultSummary.GERALD_TAGS.items()):
             node = element.find(GeraldName)
             if node is None:
                 LOGGER.info("Couldn't find %s" % (GeraldName))
@@ -414,7 +414,7 @@ def tonumber(v):
     """
     try:
         v = int(v)
-    except ValueError, e:
+    except ValueError as e:
         v = float(v)
     return v
 
@@ -442,8 +442,8 @@ def make_mean_range_element(parent, name, mean, deviation):
     Make an etree subelement <Name mean='mean', deviation='deviation'/>
     """
     element = etree.SubElement(parent, name,
-                                     { 'mean': unicode(mean),
-                                       'deviation': unicode(deviation)})
+                                     { 'mean': str(mean),
+                                       'deviation': str(deviation)})
     return element
 
 def parse_mean_range_element(element):