Initial port to python3

[htsworkflow.git] / htsworkflow / pipelines / runfolder.py

diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index 7c06e217de63d5733e524ae551f06eea40528e11..aea06a692d7d8fe12a4db43c568a44a4d8a59b3e 100644 (file)
--- a/htsworkflow/pipelines/runfolder.py
+++ b/htsworkflow/pipelines/runfolder.py
@@ -334,7 +334,7 @@ def build_gerald_runs(runs, b, image_analysis, bustard_pathname, datadir, pathna
             p.bustard = b
             p.gerald = g
             runs.append(p)
-        except IOError, e:
+        except IOError as e:
             LOGGER.error("Ignoring " + str(e))
     return len(runs) - start
 
@@ -365,7 +365,7 @@ def build_hiseq_runs(image_analysis, runs, datadir, runfolder, flowcell_id):
             if aligned:
                 p.gerald = gerald.gerald(aligned)
             runs.append(p)
-        except IOError, e:
+        except IOError as e:
             LOGGER.error("Ignoring " + str(e))
     return len(runs) - start
 
@@ -484,7 +484,7 @@ def summarize_mapped_reads(genome_map, mapped_reads):
     summarized_reads = {}
     genome_reads = 0
     genome = 'unknown'
-    for k, v in mapped_reads.items():
+    for k, v in list(mapped_reads.items()):
         path, k = os.path.split(k)
         if len(path) > 0 and path not in genome_map:
             genome = path
@@ -526,7 +526,7 @@ def summarize_lane(gerald, lane_id):
         report.append("Mapped Reads")
         mapped_reads = summarize_mapped_reads(eland_result.genome_map,
                                               eland_result.mapped_reads)
-        for name, counts in mapped_reads.items():
+        for name, counts in list(mapped_reads.items()):
             report.append("  %s: %d" % (name, counts))
 
         report.append('')