Initial port to python3

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

diff --git a/htsworkflow/pipelines/genome_mapper.py b/htsworkflow/pipelines/genome_mapper.py
index fb16d7ffc60ed70ce11c10b4a204316de9e3f37e..9162fdf26edda84fc0f520fb14d3bfa7f2c6f65f 100644 (file)
--- a/htsworkflow/pipelines/genome_mapper.py
+++ b/htsworkflow/pipelines/genome_mapper.py
@@ -30,7 +30,7 @@ def getAvailableGenomes(genome_base_dir):
   # Need valid directory
   if not os.path.exists(genome_base_dir):
     msg = "Directory does not exist: %s" % (genome_base_dir)
-    raise IOError, msg
+    raise IOError(msg)
 
   # Find all subdirectories
   filepath_list = glob.glob(os.path.join(genome_base_dir, '*'))
@@ -60,7 +60,7 @@ def getAvailableGenomes(genome_base_dir):
     build_dict = d.setdefault(species, {})
     if build in build_dict:
       msg = "Duplicate genome for %s|%s" % (species, build)
-      raise DuplicateGenome, msg
+      raise DuplicateGenome(msg)
 
     build_dict[build] = genome_dir
 
@@ -88,7 +88,7 @@ class constructMapperDict(object):
           builds = self.genome_dict[elements[0]]
 
           # sort build names the way humans would
-          keys = builds.keys()
+          keys = list(builds.keys())
           keys.sort(cmp=alphanum)
 
           # return the path from the 'last' build name
@@ -103,26 +103,26 @@ class constructMapperDict(object):
     def get(self, key, default=None):
       try:
         return self[key]
-      except KeyError, e:
+      except KeyError as e:
         return default
 
     def keys(self):
         keys = []
-        for species in self.genome_dict.keys():
+        for species in list(self.genome_dict.keys()):
             for build in self.genome_dict[species]:
                 keys.append([species+'|'+build])
         return keys
 
     def values(self):
         values = []
-        for species in self.genome_dict.keys():
+        for species in list(self.genome_dict.keys()):
             for build in self.genome_dict[species]:
                 values.append(self.genome_dict[species][build])
         return values
 
     def items(self):
         items = []
-        for species in self.genome_dict.keys():
+        for species in list(self.genome_dict.keys()):
             for build in self.genome_dict[species]:
                 key = [species+'|'+build]
                 value = self.genome_dict[species][build]
@@ -132,13 +132,13 @@ class constructMapperDict(object):
 if __name__ == '__main__':
 
   if len(sys.argv) != 2:
-    print 'useage: %s <base_genome_dir>' % (sys.argv[0])
+    print('useage: %s <base_genome_dir>' % (sys.argv[0]))
     sys.exit(1)
 
   d = getAvailableGenomes(sys.argv[1])
   d2 = constructMapperDict(d)
 
-  for k,v in d2.items():
-    print '%s: %s' % (k,v)
+  for k,v in list(d2.items()):
+    print('%s: %s' % (k,v))