def __init__(self, db_name: str):
"""
Downloader init.
:param db_name: Name of the public database to download. WARNING: must be the same spelling as in your config !
:type db_name: str
"""
# Get logging module from main script
self.logger = logging.getLogger(__name__)
# Set project config
self.config = utilities.extract_config()
# Which DB to download
self.db_name = db_name
# Download path and URL
self.dir_name = self.config[self.db_name]["SAVE FILE TO"]
self.urls = [
self.config[self.db_name][url] for url in self.config[self.db_name]
if "url" in url
]
self.filenames = [
os.path.join(self.dir_name,
url.split("/")[-1]) for url in self.urls
]
def __init__(self, db_name: str):
"""
Updater init.
:param db_name: Name of the public database to update. WARNING: must be the same spelling as in your config !
:type db_name: str
"""
# Get logging module from main script
self.logger = logging.getLogger(__name__)
# Set project config
self.config = utilities.extract_config()
# Which DB to update
self.db_name = db_name
self.species = "hsa"
self.mirna_dico = utilities.get_mirna_conversion_info(self.config)
self.gene_dico = utilities.get_gene_conversion_info(self.config)
self.unknown_mirs = []
self.unknown_genes = []
self.validated_interactions = utilities.get_validated_interactions(self.config)
# Module to convert ensemble ID necessary for RNA22
if "Rna22" in self.db_name:
self.gene_ensemble_list = []
# File paths
if "Svmicro" in self.db_name or "Mbstar" in self.db_name:
self.dir_name = self.config[self.db_name.upper()]["SAVE FILE TO"]
self.filenames = []
with open(self.config[self.db_name.upper()]["URL_0"], "r") as my_txt:
for line in my_txt:
self.filenames.append(os.path.join(self.dir_name, line).strip())
elif "Mirabel" in self.db_name:
self.dir_name = ""
self.urls = []
self.filenames = []
else:
self.dir_name = self.config[self.db_name.upper()]["SAVE FILE TO"]
self.urls = [self.config[self.db_name.upper()][url] for url in self.config[self.db_name.upper()] if "url" in url]
self.filenames = [os.path.join(self.dir_name, url.split("/")[-1]) for url in self.urls]
def __init__(self, db_list: list):
"""
Aggregator init.
:param db_list: list of databases from which to aggregate predictions
"""
# Get logging module from main script
self.logger = logging.getLogger(__name__)
# Set project config
self.config = utilities.extract_config()
# Variables
self.ascendant = [
"Targetscan", "Miranda", "Pita", "Mirmap", "Mirabel", "Rna22"
]
self.db_list = db_list
self.validated_interactions = utilities.get_validated_interactions(
self.config)
def __init__(self, db_main: str, db_compare: list):
"""
Aggregator init.
:param db_list: list of databases from which to aggregate predictions
:param db_compare: list of databases with which you wish to compare aggregated data
"""
# Get logging module from main script
self.logger = logging.getLogger(__name__)
# Set project config
self.config = utilities.extract_config()
# Variables
self.ascendant = [
"Targetscan", "Miranda", "Pita", "Mirmap", "Mirabel", "Rna22"
]
self.db_main = db_main
self.db_comp = db_compare
self.all_db = [db_main]
self.all_db.extend(self.db_comp)
self.ascendant.append(self.db_main)
from scripts import utilities
from scripts.downloader import Downloader
from scripts.updater import Updater
from scripts.aggregater import Aggregator
from scripts.rocker import Rocker
if __name__ == '__main__':
# Start execution timing
startTime = datetime.now()
# Set logging module
logging.basicConfig(level="INFO",
format="%(asctime)s - %(levelname)s - %(message)s")
# Set project config
config = utilities.extract_config()
# Set variables
parser = argparse.ArgumentParser()
parser.add_argument('-d',
action="store_true",
help="If -d present: download all files, else don't.")
parser.add_argument('-u',
action="store_true",
help="If -u present: update all files, else don't.")
parser.add_argument(
'-l',
'--list',
nargs='*',
help=
'Pass the list of databases you wish to aggregate. Default is empty list (but all DB later).',