Initial port to python3

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

diff --git a/htsworkflow/pipelines/bustard.py b/htsworkflow/pipelines/bustard.py
index 99f231dd73e748a0c88b528f4489968ab20b8428..b53813028c6e492265ca10cdf399919d04e2fec1 100644 (file)
--- a/htsworkflow/pipelines/bustard.py
+++ b/htsworkflow/pipelines/bustard.py
@@ -23,7 +23,7 @@ LOGGER = logging.getLogger(__name__)
 # make epydoc happy
 __docformat__ = "restructuredtext en"
 
-LANE_LIST = range(1,9)
+LANE_LIST = list(range(1,9))
 
 class Phasing(object):
     PHASING = 'Phasing'
@@ -111,7 +111,7 @@ class CrosstalkMatrix(object):
         for b in base_order:
             for value in self.base[b]:
                 crosstalk_value = ElementTree.SubElement(root, CrosstalkMatrix.ELEMENT)
-                crosstalk_value.text = unicode(value)
+                crosstalk_value.text = str(value)
                 crosstalk_value.tail = os.linesep
 
         return root
@@ -307,7 +307,7 @@ class Bustard(object):
 
         # add phasing parameters
         for lane in LANE_LIST:
-            if self.phasing.has_key(lane):
+            if lane in self.phasing:
                 params.append(self.phasing[lane].get_elements())
 
         # add crosstalk matrix if it exists
@@ -456,7 +456,7 @@ def main(cmdline):
     opts, args = parser.parse_args(cmdline)
 
     for bustard_dir in args:
-        print u'analyzing bustard directory: ' + unicode(bustard_dir)
+        print('analyzing bustard directory: ' + str(bustard_dir))
         bustard_object = bustard(bustard_dir)
         bustard_object.dump()
 
@@ -470,8 +470,8 @@ def main(cmdline):
         b2 = ElementTree.tostring(b2_tree).split(os.linesep)
         for line1, line2 in zip(b1, b2):
             if b1 != b2:
-                print "b1: ", b1
-                print "b2: ", b2
+                print("b1: ", b1)
+                print("b2: ", b2)
 
 if __name__ == "__main__":
     main(sys.argv[1:])