SISTR v1.1.3 release #59
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…ature and removed some serovars that will no longer be detected and reported in Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv (Soahanina, Martonos, Midway, Lindern, Bahrenfeld, Moussoro, Amberg, Madelia, Chichiri, Stafford)
…5 antigens from PulseNet and EnteroBase
…py SISTR_DB_URL global varibale with new url
… sistr/data/Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv and not via o_antigen value parsing in infer_o_antigen() sistr/sistr_cmd.py
…t. Does not delete directory anymore
…d I 1,4,[5],12:i:-
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This release updates reporting for serovars with O24-25 antigen. The O24 and O25 antigens would not be wet-lab typed reliably causing the collapse of certain serovar pairs detailed in
CHANGELOG.md. In addition users can now provide a list of serovars that their laboratory can reliably predict via the-largument and see if SISTR predicted serovar is in that list.Major updates
Soahanina,Martonos,Midway,Lindern,Bahrenfeld,Moussoro,Amberg,Madelia,ChichiriandStaffordserovars from being reported.o_antigenandantigenic_formulafields--list-of-serovarsargument allowing to check SISTR prediction against a list of selected serovars. If serovar is found in the list the result isYandNotherwiseParatyphi B,Paratyphi B var. JavaandI 1,4,[5],12:i:-serovars