Initial port to python3

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

diff --git a/htsworkflow/pipelines/genomemap.py b/htsworkflow/pipelines/genomemap.py
index fe6254e34a269ebf8d529e3d0c08547c7ec7f276..87d65eba01ff3ba51e906398b26cc385a5985c81 100644 (file)
--- a/htsworkflow/pipelines/genomemap.py
+++ b/htsworkflow/pipelines/genomemap.py
@@ -3,7 +3,7 @@
 from glob import glob
 import os
 import collections
-from htsworkflow.pipelines.runfolder import ElementTree
+from htsworkflow.pipelines import ElementTree
 
 vldInfo = collections.namedtuple('vldInfo', 'name is_link')
 
@@ -17,7 +17,7 @@ class GenomeMap(collections.MutableMapping):
         return len(self._contigs)
 
     def __iter__(self):
-        return self._contigs.iterkeys()
+        return iter(self._contigs.keys())
 
     def __getitem__(self, name):
         return self._contigs[name]
@@ -68,7 +68,7 @@ class GenomeMap(collections.MutableMapping):
 
         genome = guess_genome(sizes)
 
-        for contig, basese in sizes.items():
+        for contig, basese in list(sizes.items()):
             name = filenames[contig]
             self._contigs[name] = genome + '/' + name
 
@@ -93,6 +93,6 @@ def guess_genome(contig_sizes):
             return genomes[key][size]
 
     if len(contig_sizes) == 1:
-        return os.path.splitext(contig_sizes.keys()[0])[0]
+        return os.path.splitext(list(contig_sizes.keys())[0])[0]
 
     raise RuntimeError("Unrecognized genome type, update detection code.")