DRAM v1 DRAM_setup.py DBCAN broken download links #491
Description
Description of the bug
DRAMv1 no longer executes the setup script successfully as the DBCAN download links are broken. To circumvent this issue the links need to be updated by replacing lines 161 - 189 of database_processing.py with the following snippet. The processing file is generally found at ~/miniconda3/envs/DRAM_env/lib/python3.10/site-packages/mag_annotator/database_processing.py
def download_dbcan(output_dir='.', logger=LOGGER, dbcan_hmm=None, version=DEFAULT_DBCAN_RELEASE, verbose=True):
dbcan_hmm = path.join(output_dir, f"dbCAN-HMMdb-V{version}.txt" )
if int(version) < int(DEFAULT_DBCAN_RELEASE):
link_path = f"http://dbcan-hcc.unl.edu/download/Databases/V11/dbCAN-HMMdb-V11.txt"
else:
link_path = f"http://dbcan-hcc.unl.edu/download/Databases/V11/dbCAN-HMMdb-V11.txt"
logger.debug(f"Downloading dbCAN from: {link_path}")
download_file(link_path, dbcan_hmm, logger, verbose=verbose)
return dbcan_hmm
def download_dbcan_fam_activities (output_dir='.', logger=LOGGER, version=DEFAULT_DBCAN_RELEASE, upload_date=DEFAULT_DBCAN_DATE,
verbose=True):
dbcan_fam_activities = path.join(output_dir, f'CAZyDB.{upload_date}.fam-activities.txt')
url = f"http://dbcan-hcc.unl.edu/download/Databases/V11/CAZyDB.08062022.fam-activities.txt"
logger.info(f"Downloading dbCAN family activities from : {url}")
download_file(url, dbcan_fam_activities, logger, verbose=verbose)
return dbcan_fam_activities
def download_dbcan_subfam_ec(output_dir='.', logger=LOGGER, version=DEFAULT_DBCAN_RELEASE, upload_date=DEFAULT_DBCAN_DATE, verbose=True):
dbcan_subfam_ec = path.join(output_dir, f"CAZyDB.{upload_date}.fam.subfam.ec.txt")
url = (f"http://dbcan-hcc.unl.edu/download/Databases/"
f"V{version}/CAZyDB.{upload_date}.fam.subfam.ec.txt")
logger.info(f"Downloading dbCAN sub-family encumber from : {url}")
download_file(url, dbcan_subfam_ec, logger, verbose=verbose)
return dbcan_subfam_ec
System information
DRAM_setup.py
Command used and terminal output
Relevant files
No response