# 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, '*'))
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
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
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]
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))