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)) grsnp_path.write_treeview_json(os.path.join(db_dir, org)) self._index_html = {}