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Initial port to python3
[htsworkflow.git]
/
htsworkflow
/
pipelines
/
ipar.py
diff --git
a/htsworkflow/pipelines/ipar.py
b/htsworkflow/pipelines/ipar.py
index f818b3495fbf2fd2d8f2fba13d698188e7680d3f..576bff85aedba54c2cd01b0e0c12d2c18aff5b06 100644
(file)
--- a/
htsworkflow/pipelines/ipar.py
+++ b/
htsworkflow/pipelines/ipar.py
@@
-52,11
+52,11
@@
class Tiles(object):
return value_list
def items(self):
return value_list
def items(self):
- return
zip(self.keys(), self.values(
))
+ return
list(zip(list(self.keys()), list(self.values())
))
def __getitem__(self, key):
# FIXME: this is inefficient. building the dictionary be rescanning the xml.
def __getitem__(self, key):
# FIXME: this is inefficient. building the dictionary be rescanning the xml.
- v = dict(
self.items(
))
+ v = dict(
list(self.items()
))
return v[key]
class IPAR(object):
return v[key]
class IPAR(object):
@@
-146,12
+146,12
@@
class IPAR(object):
"""
suffix_node = self.tree.find('RunParameters/CompressionSuffix')
if suffix_node is None:
"""
suffix_node = self.tree.find('RunParameters/CompressionSuffix')
if suffix_node is None:
- print
"find compression suffix failed"
+ print
("find compression suffix failed")
return None
suffix = suffix_node.text
files = []
format = "%s_%s_%04d_%s.txt%s"
return None
suffix = suffix_node.text
files = []
format = "%s_%s_%04d_%s.txt%s"
- for lane, attrib in
self.tiles.items(
):
+ for lane, attrib in
list(self.tiles.items()
):
for file_type in ["int","nse"]:
start, stop = attrib['TileRange']
for tile in range(start, stop+1):
for file_type in ["int","nse"]:
start, stop = attrib['TileRange']
for tile in range(start, stop+1):
@@
-159,8
+159,8
@@
class IPAR(object):
return files
def dump(self):
return files
def dump(self):
- print
"Matrix:", self.matrix
- print
"Tree:", self.tree
+ print
("Matrix:", self.matrix)
+ print
("Tree:", self.tree)
def get_elements(self):
attribs = {'version': str(IPAR.XML_VERSION) }
def get_elements(self):
attribs = {'version': str(IPAR.XML_VERSION) }
@@
-195,7
+195,7
@@
def load_ipar_param_tree(paramfile):
tree = ElementTree.parse(paramfile).getroot()
run = tree.find('Run')
tree = ElementTree.parse(paramfile).getroot()
run = tree.find('Run')
- if
run.attrib.has_key('Name')
and run.attrib['Name'] in SOFTWARE_NAMES:
+ if
'Name' in run.attrib
and run.attrib['Name'] in SOFTWARE_NAMES:
return run
else:
LOGGER.info("No run found")
return run
else:
LOGGER.info("No run found")