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Initial port to python3
[htsworkflow.git]
/
htsworkflow
/
submission
/
geo.py
diff --git
a/htsworkflow/submission/geo.py
b/htsworkflow/submission/geo.py
index ef8d9457218a76ce53f0872f44efafd6d478dea1..20a56a06ff7fad01a36cd9f9325ad342acf0ca4f 100644
(file)
--- a/
htsworkflow/submission/geo.py
+++ b/
htsworkflow/submission/geo.py
@@
-28,7
+28,7
@@
class GEOSubmission(Submission):
series = self.get_series_metadata()
series_attribs = dict(series)
series_id = series_attribs['^series']
series = self.get_series_metadata()
series_attribs = dict(series)
series_id = series_attribs['^series']
- for lib_id, result_dir in
result_map.items(
):
+ for lib_id, result_dir in
list(result_map.items()
):
an_analysis = self.get_submission_node(result_dir)
metadata = self.get_sample_metadata(an_analysis)
if len(metadata) == 0:
an_analysis = self.get_submission_node(result_dir)
metadata = self.get_sample_metadata(an_analysis)
if len(metadata) == 0:
@@
-52,7
+52,7
@@
class GEOSubmission(Submission):
'platform_id': platform_id,
'series_id': series_id,
})
'platform_id': platform_id,
'series_id': series_id,
})
- print
str(soft_template.render(context
))
+ print
(str(soft_template.render(context)
))
def check_for_name(self, analysis_node):
name = fromTypedNode(
def check_for_name(self, analysis_node):
name = fromTypedNode(
@@
-129,12
+129,12
@@
class GEOSubmission(Submission):
lanes = {}
for row in self.execute_query(query_template, context):
data = {}
lanes = {}
for row in self.execute_query(query_template, context):
data = {}
- for k, v in
row.items(
):
+ for k, v in
list(row.items()
):
data[k] = v
library = str(data['library'])
lanes.setdefault(library, []).append(data)
result = []
data[k] = v
library = str(data['library'])
lanes.setdefault(library, []).append(data)
result = []
- for library, files in l
anes.items(
):
+ for library, files in l
ist(lanes.items()
):
if len(files) > 2:
errmsg = "Don't know what to do with more than 2 raw files"
raise ValueError(errmsg)
if len(files) > 2:
errmsg = "Don't know what to do with more than 2 raw files"
raise ValueError(errmsg)