def get_resources(genome, ref_file, data):
"""Retrieve genome information from a genome-references.yaml file.
"""
base_dir = os.path.normpath(os.path.dirname(ref_file))
resource_file = os.path.join(base_dir, "%s-resources.yaml" % genome.replace("-test", ""))
if not os.path.exists(resource_file):
raise IOError("Did not find resource file for %s: %s\n"
"To update bcbio_nextgen.py with genome resources for standard builds, run:\n"
"bcbio_nextgen.py upgrade -u skip"
% (genome, resource_file))
with open(resource_file) as in_handle:
resources = yaml.load(in_handle)
def resource_file_path(x):
if isinstance(x, basestring) and os.path.exists(os.path.join(base_dir, x)):
return os.path.normpath(os.path.join(base_dir, x))
return x
cleaned = utils.dictapply(resources, resource_file_path)
return ensure_annotations(cleaned, data)
def get_resources(genome, ref_file):
"""Retrieve genome information from a genome-references.yaml file.
"""
base_dir = os.path.normpath(os.path.dirname(ref_file))
resource_file = os.path.join(base_dir, "%s-resources.yaml" % genome.replace("-test", ""))
if not os.path.exists(resource_file):
raise IOError("Did not find resource file for %s: %s\n"
"To update bcbio_nextgen.py with genome resources for standard builds, run:\n"
"bcbio_nextgen.py upgrade -u skip"
% (genome, resource_file))
with open(resource_file) as in_handle:
resources = yaml.load(in_handle)
def resource_file_path(x):
if isinstance(x, basestring) and os.path.exists(os.path.join(base_dir, x)):
return os.path.normpath(os.path.join(base_dir, x))
return x
return utils.dictapply(resources, resource_file_path)
