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updated readme with updated sistr database url
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kbessonov1984 committed Dec 3, 2024
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2 changes: 1 addition & 1 deletion README.rst
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Expand Up @@ -127,7 +127,7 @@ SISTR will automatically initialize database of *Salmonella* serovar determinati
The SISTR database v1.3 got minor updates by collapsing some of the serovars with O24/O25 antigens detailed in `CHANGELOG.md <CHANGELOG.md>`_ file

- SISTR v1.1 database is available at https://zenodo.org/records/13618515 or via a direct url https://zenodo.org/records/13618515/files/SISTR_V_1.1_db.tar.gz?download=1 (used with SISTR < 1.1.3 )
- SISTR v1.3 database is available at https://zenodo.org/records/13693495 or va a direct url https://zenodo.org/records/13693495/files/SISTR_V_1.1.3_db.tar.gz?download=1 (used with SISTR >= 1.1.3)
- SISTR v1.3 database is available at https://zenodo.org/records/14270992 or va a direct url https://zenodo.org/records/14270992/files/SISTR_V_1.1.3_db.tar.gz?download=1 (used with SISTR >= 1.1.3)


Dependencies
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2 changes: 1 addition & 1 deletion sistr/src/serovar_prediction/constants.py
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CGMLST_SUBSPECIATION_DISTANCE_THRESHOLD = 0.9
MASH_SUBSPECIATION_DISTANCE_THRESHOLD = 0.01

SISTR_DB_URL = 'https://zenodo.org/records/13693495/files/SISTR_V_1.1.3_db.tar.gz?download=1'
SISTR_DB_URL = 'https://zenodo.org/records/14270992/files/SISTR_V_1.1.3_db.tar.gz?download=1'
SISTR_DATA_DIR = resource_filename('sistr','data')
SEROVAR_TABLE_PATH = resource_filename('sistr', 'data/Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv')
WZX_FASTA_PATH = resource_filename('sistr', 'data/antigens/wzx.fasta')
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