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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,
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 end in self.lane_results:
- for lane in
end.values(
):
+ for lane in
list(end.values()
):
summary.append(lane.get_elements())
return summary
summary.append(lane.get_elements())
return summary
@@
-67,7
+67,7
@@
class Summary(object):
Debugging function, report current object
"""
tree = self.get_elements()
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):
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:
('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:
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,
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
value = getattr(self, variable_name)
if value is None:
continue
# it looks like a sequence
- elif type(value) in (t
ypes.TupleType, types.ListType
):
+ elif type(value) in (t
uple, list
):
element = make_mean_range_element(
lane_result,
tag,
element = make_mean_range_element(
lane_result,
tag,
@@
-294,7
+294,7
@@
class LaneResultSummary(object):
)
else:
element = etree.SubElement(lane_result, tag)
)
else:
element = etree.SubElement(lane_result, tag)
- element.text =
unicode
(value)
+ element.text =
str
(value)
return lane_result
def set_elements(self, tree):
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))
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,))
LOGGER.warn('Unrecognized tag %s' % (element.tag,))
@@
-333,7
+333,7
@@
class LaneResultSummaryGA(LaneResultSummary):
else:
self.lane_yield = None
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))
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)
"""
try:
v = int(v)
- except ValueError
,
e:
+ except ValueError
as
e:
v = float(v)
return v
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,
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):
return element
def parse_mean_range_element(element):