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 d29e44640b233c6cdc201e24c26ae5c781ae2891..9162fdf26edda84fc0f520fb14d3bfa7f2c6f65f 100644 (file)
--- a/htsworkflow/pipelines/genome_mapper.py
+++ b/htsworkflow/pipelines/genome_mapper.py
@@ -8,6 +8,7 @@ import logging
 
 from htsworkflow.util.alphanum import alphanum
 
+LOGGER = logging.getLogger(__name__)
 class DuplicateGenome(Exception): pass
 
 
@@ -22,14 +23,14 @@ def getAvailableGenomes(genome_base_dir):
   """
   raises IOError (on genome_base_dir not found)
   raises DuplicateGenome on duplicate genomes found.
-  
+
   returns a double dictionary (i.e. d[species][build] = path)
   """
 
   # 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, '*'))
@@ -52,90 +53,92 @@ def getAvailableGenomes(genome_base_dir):
     try:
       species, build = line.split('|')
     except:
-      logging.warning('Skipping: Invalid metafile (%s) line: %s' \
-                      % (metafile, line))
+      LOGGER.warning('Skipping: Invalid metafile (%s) line: %s' \
+                     % (metafile, line))
       continue
 
     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
 
   return d
-  
+
 
 class constructMapperDict(object):
     """
     Emulate a dictionary to map genome|build names to paths.
-    
+
     It uses the dictionary generated by getAvailableGenomes.
     """
     def __init__(self, genome_dict):
         self.genome_dict = genome_dict
-        
+
     def __getitem__(self, key):
         """
         Return the best match for key
         """
         elements = re.split("\|", key)
-        
-        try:  
-            if len(elements) == 1:
-                # we just the species name
-                # get the set of builds
-                builds = self.genome_dict[elements[0]]
-            
-                # sort build names the way humans would
-                keys = builds.keys()
-                keys.sort(cmp=alphanum)
-            
-                # return the path from the 'last' build name
-                return builds[keys[-1]]
-                        
-            elif len(elements) == 2:
-                # we have species, and build name
-                return self.genome_dict[elements[0]][elements[1]]
-            else:
-                raise KeyError("Unrecognized key")
-        except KeyError, e:
-            logging.error('Unrecognized genome identifier: %s' % str((elements),))
-            return "NoGenomeAvailable"
-        
+
+        if len(elements) == 1:
+          # we just the species name
+          # get the set of builds
+          builds = self.genome_dict[elements[0]]
+
+          # sort build names the way humans would
+          keys = list(builds.keys())
+          keys.sort(cmp=alphanum)
+
+          # return the path from the 'last' build name
+          return builds[keys[-1]]
+
+        elif len(elements) == 2:
+          # we have species, and build name
+          return self.genome_dict[elements[0]][elements[1]]
+        else:
+          raise KeyError("Unrecognized key")
+
+    def get(self, key, default=None):
+      try:
+        return self[key]
+      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]
                 items.append((key, value))
         return items
-            
+
 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))
+
+