def __init__(self):
# go through each database directory and create custom_data if it does not exist.
for db_ver,db_dir in sett["data_dir"].items():
# create all directories in the custom_data dir if they do not already exist
for org in self.get_org(db_ver):
custom_dir = os.path.join(os.path.split(db_dir)[0],"custom_data")
logger.info("Processing genomic features for {}".format(org))
if not os.path.exists(custom_dir): os.mkdir(custom_dir)
cust_sub_dir = ["backgrounds","gfs","fois","rsid_conversion"]
for c in cust_sub_dir:
tmp = os.path.join(custom_dir,c)
if not os.path.exists(tmp): os.mkdir(tmp)
c_dir = os.path.join(custom_dir,c,org)
if not os.path.exists(c_dir): os.mkdir(c_dir)
# Read the genomic feature files and generate html files
paths = PathNode()
paths.name = "Root"
paths.organisms = self.get_org(db_ver)
paths.traverse(os.path.join(db_dir,org))
paths.write_treeview_html(db_dir,org)
self._index_html = {}
def __init__(self):
# go through each database directory and create custom_data if it does not exist.
for db_ver, db_dir in sett["data_dir"].items():
# create all directories in the custom_data dir if they do not already exist
for org in self.get_org(db_ver):
custom_dir = os.path.join(
os.path.split(db_dir)[0], "custom_data")
logger.info("Processing genomic features for {}".format(org))
if not os.path.exists(custom_dir): os.mkdir(custom_dir)
cust_sub_dir = [
"backgrounds", "gfs", "fois", "rsid_conversion"
]
for c in cust_sub_dir:
tmp = os.path.join(custom_dir, c)
if not os.path.exists(tmp): os.mkdir(tmp)
c_dir = os.path.join(custom_dir, c, org)
if not os.path.exists(c_dir): os.mkdir(c_dir)
# Read the genomic feature files and generate html files
paths = PathNode()
paths.name = "Root"
paths.organisms = self.get_org(db_ver)
paths.traverse(os.path.join(db_dir, org))
paths.write_treeview_html(db_dir, org)
self._index_html = {}
