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Initial port to python3
[htsworkflow.git]
/
htsworkflow
/
pipelines
/
eland.py
diff --git
a/htsworkflow/pipelines/eland.py
b/htsworkflow/pipelines/eland.py
index a508a494c8c24900e8574c75f43c3616bf309814..feb7ff7c066ea070b836f47ce4d03536b8416095 100644
(file)
--- a/
htsworkflow/pipelines/eland.py
+++ b/
htsworkflow/pipelines/eland.py
@@
-376,7
+376,7
@@
class ElandLane(ResultLane):
def get_elements(self):
lane = ElementTree.Element(ElandLane.LANE,
{'version':
def get_elements(self):
lane = ElementTree.Element(ElandLane.LANE,
{'version':
-
unicode
(ElandLane.XML_VERSION)})
+
str
(ElandLane.XML_VERSION)})
sample_tag = ElementTree.SubElement(lane, SAMPLE_NAME)
sample_tag.text = self.sample_name
lane_tag = ElementTree.SubElement(lane, LANE_ID)
sample_tag = ElementTree.SubElement(lane, SAMPLE_NAME)
sample_tag.text = self.sample_name
lane_tag = ElementTree.SubElement(lane, LANE_ID)
@@
-385,22
+385,22
@@
class ElandLane(ResultLane):
end_tag = ElementTree.SubElement(lane, END)
end_tag.text = str(self.end)
genome_map = ElementTree.SubElement(lane, GENOME_MAP)
end_tag = ElementTree.SubElement(lane, END)
end_tag.text = str(self.end)
genome_map = ElementTree.SubElement(lane, GENOME_MAP)
- for k, v in
self.genome_map.items(
):
+ for k, v in
list(self.genome_map.items()
):
item = ElementTree.SubElement(
genome_map, GENOME_ITEM,
item = ElementTree.SubElement(
genome_map, GENOME_ITEM,
- {'name':k, 'value':
unicode
(v)})
+ {'name':k, 'value':
str
(v)})
mapped_reads = ElementTree.SubElement(lane, MAPPED_READS)
mapped_reads = ElementTree.SubElement(lane, MAPPED_READS)
- for k, v in
self.mapped_reads.items(
):
+ for k, v in
list(self.mapped_reads.items()
):
item = ElementTree.SubElement(
mapped_reads, MAPPED_ITEM,
item = ElementTree.SubElement(
mapped_reads, MAPPED_ITEM,
- {'name':k, 'value':
unicode
(v)})
+ {'name':k, 'value':
str
(v)})
match_codes = ElementTree.SubElement(lane, MATCH_CODES)
match_codes = ElementTree.SubElement(lane, MATCH_CODES)
- for k, v in
self.match_codes.items(
):
+ for k, v in
list(self.match_codes.items()
):
item = ElementTree.SubElement(
match_codes, MATCH_ITEM,
item = ElementTree.SubElement(
match_codes, MATCH_ITEM,
- {'name':k, 'value':
unicode
(v)})
+ {'name':k, 'value':
str
(v)})
reads = ElementTree.SubElement(lane, READS)
reads = ElementTree.SubElement(lane, READS)
- reads.text =
unicode
(self.reads)
+ reads.text =
str
(self.reads)
return lane
return lane
@@
-457,7
+457,7
@@
class MatchCodes(collections.MutableMapping):
for key in initializer:
if key not in self.match_codes:
errmsg = "Initializer can only contain: %s"
for key in initializer:
if key not in self.match_codes:
errmsg = "Initializer can only contain: %s"
- raise ValueError(errmsg % (",".join(
self.match_codes.keys(
))))
+ raise ValueError(errmsg % (",".join(
list(self.match_codes.keys()
))))
self.match_codes[key] += initializer[key]
def __iter__(self):
self.match_codes[key] += initializer[key]
def __iter__(self):
@@
-472,7
+472,7
@@
class MatchCodes(collections.MutableMapping):
def __setitem__(self, key, value):
if key not in self.match_codes:
errmsg = "Unrecognized key, allowed values are: %s"
def __setitem__(self, key, value):
if key not in self.match_codes:
errmsg = "Unrecognized key, allowed values are: %s"
- raise ValueError(errmsg % (",".join(
self.match_codes.keys(
))))
+ raise ValueError(errmsg % (",".join(
list(self.match_codes.keys()
))))
self.match_codes[key] = value
def __len__(self):
self.match_codes[key] = value
def __len__(self):
@@
-483,7
+483,7
@@
class MatchCodes(collections.MutableMapping):
raise ValueError("Expected a MatchCodes, got %s", str(type(other)))
newobj = MatchCodes(self)
raise ValueError("Expected a MatchCodes, got %s", str(type(other)))
newobj = MatchCodes(self)
- for key, value in
other.items(
):
+ for key, value in
list(other.items()
):
newobj[key] = self.get(key, 0) + other[key]
return newobj
newobj[key] = self.get(key, 0) + other[key]
return newobj
@@
-574,7
+574,7
@@
class SequenceLane(ResultLane):
LOGGER.info("summarizing results for %s" % (pathname))
lines = 0
f = open(pathname)
LOGGER.info("summarizing results for %s" % (pathname))
lines = 0
f = open(pathname)
- for l in f
.xreadlines()
:
+ for l in f:
lines += 1
f.close()
lines += 1
f.close()
@@
-589,7
+589,7
@@
class SequenceLane(ResultLane):
def get_elements(self):
lane = ElementTree.Element(SequenceLane.LANE,
{'version':
def get_elements(self):
lane = ElementTree.Element(SequenceLane.LANE,
{'version':
-
unicode
(SequenceLane.XML_VERSION)})
+
str
(SequenceLane.XML_VERSION)})
sample_tag = ElementTree.SubElement(lane, SAMPLE_NAME)
sample_tag.text = self.sample_name
lane_tag = ElementTree.SubElement(lane, LANE_ID)
sample_tag = ElementTree.SubElement(lane, SAMPLE_NAME)
sample_tag.text = self.sample_name
lane_tag = ElementTree.SubElement(lane, LANE_ID)
@@
-598,16
+598,16
@@
class SequenceLane(ResultLane):
end_tag = ElementTree.SubElement(lane, END)
end_tag.text = str(self.end)
reads = ElementTree.SubElement(lane, READS)
end_tag = ElementTree.SubElement(lane, END)
end_tag.text = str(self.end)
reads = ElementTree.SubElement(lane, READS)
- reads.text =
unicode
(self.reads)
+ reads.text =
str
(self.reads)
sequence_type = ElementTree.SubElement(lane, SequenceLane.SEQUENCE_TYPE)
sequence_type = ElementTree.SubElement(lane, SequenceLane.SEQUENCE_TYPE)
- sequence_type.text =
unicode
(SequenceLane.SEQUENCE_DESCRIPTION[self.sequence_type])
+ sequence_type.text =
str
(SequenceLane.SEQUENCE_DESCRIPTION[self.sequence_type])
return lane
def set_elements(self, tree):
if tree.tag != SequenceLane.LANE:
raise ValueError('Exptecting %s' % (SequenceLane.LANE,))
return lane
def set_elements(self, tree):
if tree.tag != SequenceLane.LANE:
raise ValueError('Exptecting %s' % (SequenceLane.LANE,))
- lookup_sequence_type = dict([ (v,k) for k,v in
SequenceLane.SEQUENCE_DESCRIPTION.items(
)])
+ lookup_sequence_type = dict([ (v,k) for k,v in
list(SequenceLane.SEQUENCE_DESCRIPTION.items()
)])
for element in tree:
tag = element.tag.lower()
for element in tree:
tag = element.tag.lower()
@@
-657,7
+657,7
@@
class ELAND(collections.MutableMapping):
del self.result[key]
def __iter__(self):
del self.result[key]
def __iter__(self):
- keys =
self.results.iterkeys(
)
+ keys =
iter(self.results.keys()
)
for k in sorted(keys):
yield k
for k in sorted(keys):
yield k
@@
-670,18
+670,18
@@
class ELAND(collections.MutableMapping):
raise ValueError("Key must be a %s" % (str(type(SampleKey))))
if not search.iswild:
yield self[search]
raise ValueError("Key must be a %s" % (str(type(SampleKey))))
if not search.iswild:
yield self[search]
- for key in
self.keys(
):
+ for key in
list(self.keys()
):
if key.matches(search): yield key
def get_elements(self):
root = ElementTree.Element(ELAND.ELAND,
if key.matches(search): yield key
def get_elements(self):
root = ElementTree.Element(ELAND.ELAND,
- {'version':
unicode
(ELAND.XML_VERSION)})
+ {'version':
str
(ELAND.XML_VERSION)})
for key in self:
eland_lane = self[key].get_elements()
for key in self:
eland_lane = self[key].get_elements()
- eland_lane.attrib[ELAND.END] =
unicode
(self[key].end-1)
- eland_lane.attrib[ELAND.LANE_ID] =
unicode
(self[key].lane_id)
- eland_lane.attrib[ELAND.SAMPLE] =
unicode
(self[key].sample_name)
+ eland_lane.attrib[ELAND.END] =
str
(self[key].end-1)
+ eland_lane.attrib[ELAND.LANE_ID] =
str
(self[key].lane_id)
+ eland_lane.attrib[ELAND.SAMPLE] =
str
(self[key].sample_name)
root.append(eland_lane)
return root
return root
root.append(eland_lane)
return root
return root
@@
-895,7
+895,7
@@
def main(cmdline=None):
for a in args:
LOGGER.info("Starting scan of %s" % (a,))
e = eland(a)
for a in args:
LOGGER.info("Starting scan of %s" % (a,))
e = eland(a)
- print
ElementTree.tostring(e.get_elements(
))
+ print
(ElementTree.tostring(e.get_elements()
))
return
return