# This file is part of Sequana software
#
# Copyright (c) 2016-2021 - Sequana Development Team
#
#
# Distributed under the terms of the 3-clause BSD license.
# The full license is in the LICENSE file, distributed with this software.
#
# website: https://github.com/sequana/sequana
# documentation: http://sequana.readthedocs.io
#
##############################################################################
import os
from pathlib import Path
import colorlog
from easydev import md5
from sequana import sequana_config_path
from sequana.misc import download
logger = colorlog.getLogger(__name__)
__all__ = [
"KrakenDownload",
]
[docs]
class KrakenDownload(object):
"""Utility to download Kraken DB and place them in a local directory
::
from sequana import KrakenDownload
kd = KrakenDownload()
kd.download('toydb')
"""
def __init__(self, output_dir=None):
if output_dir is None: # pragma: no cover
self.output_dir = Path(f"{sequana_config_path}") / "kraken2_dbs"
else:
self.output_dir = Path(output_dir)
[docs]
def download(self, name):
base = self.output_dir / f"{name}"
base.mkdir(exist_ok=True, parents=True)
dbs = {
"archaea_masking:v21.1.1": {
"record": 12542771,
"md5sum": [
"915c432508468e447d1c6baf6ffc830e",
"09f563c3bea7016eff9183fb09217758",
"72442300b21711b4fa2a8365b5ee7296",
],
},
"bacteria_masking:v21.1.1": {
"record": 11518607,
"md5sum": [
"25c352ca110df1dee1c8f21c3ac53967",
"05b0f7e1a1b0f3e27168103d5b5ff9d2",
"7d1d12ae10136401eb415456309a8ccb",
],
},
"bacteria_masking:v24.4.4": {
"record": 11519701,
"md5sum": [
"9b2ece5637ce6386ed5acff95cd67207",
"16ecf13836be8aed41e97621f2dae962",
"5a8a0f28861eb04d4fab18b277469430",
],
},
"fungi_masking:v21.1.1": {
"record": 11519096,
"md5sum": [
"92f90da86ca8a9e2b668441d80f6c910",
"c3107537fe69672bdee7106c93655fe3",
"522442126d9a49450cc799bf81de2dc3",
],
},
"fungi_masking:v24.3.15": {
"record": 11519079,
"md5sum": [
"5635040a6120502069d6f34640406409",
"16ecf13836be8aed41e97621f2dae962",
"f6865f8579296980ddfe5eae3edf4ed2",
],
},
"human_masking:v21.1.1": {
"record": 12531542,
"md5sum": [
"8858d7095d6d63bbe6130aff058179f9",
"5fc44bb53c331e806b74293c5ae6958e",
"46a3c6350015c9ea633961915dfed387",
],
},
"plasmid_masking:v24.8.20": {
"record": 13349404,
"md5sum": [
"de0d9f50a6166d7577e28e40e6fd82b1",
"5ac9bf4fa2065244f76f6f126aa8104a",
"b24b8fb355b63065b24542f006f5221e",
],
},
"plastid_masking:v24.8.20": {
"record": 13351786,
"md5sum": [
"0e531e989673e5967f3596c0affe9280",
"5ac9bf4fa2065244f76f6f126aa8104a",
"b24b8fb355b63065b24542f006f5221e",
],
},
"protozoa_masking:v24.8.1": {
"record": 13351751,
"md5sum": [
"2b1186d1f95a0b00ce402a205ea1bcd9",
"4b6c1f6ab2e084eef5b59e64788b39c1",
"8fc0899aeea7e9822742f54b480a3c24",
],
},
"viruses_masking:v21.1.1": {
"record": 10947729,
"md5sum": [
"a159efd713abd151d7dfc78327ae47f9",
"dc786f571c76d1c0c568c6dd7a701160",
"6fde7647f2cc02499035dfef5f615eab",
],
},
"viruses_masking:v24.1.31": { # pragma: no cover
"record": 10947714,
"md5sum": [
"4607d25e898de1dc9f2cea63392d291c",
"c8771f5abed9149983cc435efc597bed",
"4826a642ee55ba4301b7bcd1b983471d",
],
},
"toydb": {
"record": 10829308,
"md5sum": [
"31f4b20f9e5c6beb9e1444805264a6e5",
"733f7587f9c0c7339666d5906ec6fcd3",
"7bb56a0f035b27839fb5c18590b79263",
],
},
"covid_masking:v1": {
"record": 12542612,
"md5sum": [
"fb3a3f7300dbdcc452594d2d220de6ea",
"1365cf454f8a7634bcce785133af3dbb",
"16022f7af01e84e5a6ea7fac4640b1b5",
],
},
"mmu38_masking:v21": {"record": 1, "md5sum": ["", "", ""]},
"mmu38_masking:v24": {"record": 1, "md5sum": ["", "", ""]},
}
if name in dbs.keys():
record = dbs[name]["record"]
md5sums = dbs[name]["md5sum"]
links = [f"https://zenodo.org/records/{record}/files/{x}" for x in ["hash.k2d", "opts.k2d", "taxo.k2d"]]
else:
raise ValueError(f"{name} not a valid/known database")
for link, md5sum in zip(links, md5sums):
basename = link.split("/")[-1]
filename = base / basename
if os.path.exists(filename) and md5(filename) == md5sum:
logger.warning(f"{filename} already present with expected md5sum")
else:
logger.info(f"Downloading {link}")
download(link, filename)
