Initial port to python3

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

diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py
index 75d7d2e514485503b0cca1a612a969ddc6e156e0..2d5d3d51a05e7fddc222b54d1dd2e3384e7af984 100644 (file)
--- a/htsworkflow/pipelines/gerald.py
+++ b/htsworkflow/pipelines/gerald.py
@@ -12,7 +12,7 @@ from htsworkflow.pipelines.summary import Summary, SummaryGA, SummaryHiSeq
 from htsworkflow.pipelines.eland import eland, ELAND
 from htsworkflow.pipelines.samplekey import SampleKey
 
-from htsworkflow.pipelines.runfolder import \
+from htsworkflow.pipelines import \
    ElementTree, \
    EUROPEAN_STRPTIME, \
    LANES_PER_FLOWCELL, \
@@ -59,10 +59,10 @@ class Alignment(object):
         """
         Debugging function, report current object
         """
-        print 'Software:'. self.__class__.__name__
-        print 'Alignment version:', self.version
-        print 'Run date:', self.date
-        print 'config.xml:', self.tree
+        print('Software:'. self.__class__.__name__)
+        print('Alignment version:', self.version)
+        print('Run date:', self.date)
+        print('config.xml:', self.tree)
         self.summary.dump()
 
     def get_elements(self, root_tag):
@@ -70,7 +70,7 @@ class Alignment(object):
             return None
 
         gerald = ElementTree.Element(root_tag,
-                                     {'version': unicode(Gerald.XML_VERSION)})
+                                     {'version': str(Gerald.XML_VERSION)})
         gerald.append(self.tree)
         gerald.append(self.summary.get_elements())
         if self.eland_results:
@@ -177,7 +177,7 @@ class CASAVA(Alignment):
         if self.tree is None:
             return
         if len(self.tree.xpath('TIME_STAMP')) == 0:
-            time_stamp = self.date.strftime("%a %b %d %H:%M:%S %Y")
+            time_stamp = self.date.strftime('%a %b %d %H:%M:%S %Y')
             time_element = ElementTree.Element('TIME_STAMP')
             time_element.text = time_stamp
             self.tree.append(time_element)
@@ -283,7 +283,7 @@ class LaneParametersGA(LaneParameters):
         lanes = [x.tag.split('_')[1] for x in container.getchildren()]
         try:
             index = lanes.index(self._lane_id)
-        except ValueError, e:
+        except ValueError as e:
             return None
         element = container[index]
         return element.text
@@ -397,7 +397,7 @@ class LaneSpecificRunParameters(collections.MutableMapping):
     def __iter__(self):
         if self._lanes is None:
             self._initialize_lanes()
-        return self._lanes.iterkeys()
+        return iter(self._lanes.keys())
 
     def __getitem__(self, key):
         if self._lanes is None:
@@ -410,7 +410,7 @@ class LaneSpecificRunParameters(collections.MutableMapping):
             return self._lanes[real_key]
         raise KeyError("%s not found in %s" % (
             repr(key),
-            ",".join((repr(k) for k in self._lanes.keys()))))
+            ",".join((repr(k) for k in list(self._lanes.keys())))))
 
     def __setitem__(self, key, value):
         if len(self._lanes) > 100: