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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"
# make epydoc happy
__docformat__ = "restructuredtext en"
-LANE_LIST =
range(1,9
)
+LANE_LIST =
list(range(1,9)
)
class Phasing(object):
PHASING = 'Phasing'
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)
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
crosstalk_value.tail = os.linesep
return root
@@
-307,7
+307,7
@@
class Bustard(object):
# add phasing parameters
for lane in LANE_LIST:
# 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
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:
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()
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:
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:])
if __name__ == "__main__":
main(sys.argv[1:])