From 7d2d591d4b453eb4dd4af9a62a03c0d6ca60d2b0 Mon Sep 17 00:00:00 2001 From: Vedanth Date: Mon, 19 Aug 2024 14:43:00 +0530 Subject: [PATCH] Update SARG db link in crude_db_harmonisation The SARG database link was broken (https://github.com/xinehc/args_oap/issues/69), so another link to SARG db from its argsoap github repo is now used (https://github.com/xinehc/args_oap/blob/main/src/args_oap/db/sarg.fasta) --- db_harmonisation/crude_db_harmonisation.py | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/db_harmonisation/crude_db_harmonisation.py b/db_harmonisation/crude_db_harmonisation.py index 9950f50..59ff409 100644 --- a/db_harmonisation/crude_db_harmonisation.py +++ b/db_harmonisation/crude_db_harmonisation.py @@ -37,16 +37,9 @@ def get_resfinder_db(): url = 'https://bitbucket.org/genomicepidemiology/resfinder_db/raw/8aad1d20603fbec937cdae55024568de6dbd609f/all.fsa' return download_file(url, ofile) -@TaskGenerator def get_sarg_db(): - with tempfile.TemporaryDirectory() as tmpdir: - tmp_zip = f'{tmpdir}/Short_subdatabase_V3.2.1.zip' - download_file.f('https://smile.hku.hk/ARGs/dataset/indexingdownload/Short_subdatabase_V3.2.1.zip', tmp_zip) - subprocess.check_call( - ['unzip', tmp_zip, '-d', tmpdir]) - shutil.copy(f'{tmpdir}/Short_subdatabase/4.SARG_v3.2_20220917_Short_subdatabase.fasta', 'dbs/sarg.faa') - - return 'dbs/sarg.faa' + url = 'https://raw.githubusercontent.com/xinehc/args_oap/a3e5cff4a6c09f81e4834cfd9a31e6ce7d678d71/src/args_oap/db/sarg.fasta' + return download_file(url, 'dbs/sarg.faa') def get_deeparg_db(): url = 'https://bitbucket.org/gusphdproj/deeparg-largerepo/raw/5683ea1c075dad3a68e0e236c98e2a98d564f560/database/v2/features.fasta'