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']
-        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:
@@ -52,7 +52,7 @@ class GEOSubmission(Submission):
             '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(
@@ -129,12 +129,12 @@ class GEOSubmission(Submission):
         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 = []
-        for library, files in lanes.items():
+        for library, files in list(lanes.items()):
             if len(files) > 2:
                 errmsg = "Don't know what to do with more than 2 raw files"
                 raise ValueError(errmsg)