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Update SARG db link in crude_db_harmonisation #64

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Aug 19, 2024
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Update SARG db link in crude_db_harmonisation #64

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11 changes: 2 additions & 9 deletions db_harmonisation/crude_db_harmonisation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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'
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