pipeline bug fixes: astrovirus for eid2; virus sp. for gmpd

viralemergence · Aug 5, 2021 · 2604d22 · 2604d22
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commit 2604d22
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diff --git a/clover/clover_0.1_mammalviruses/CLOVER_0.1_MammalViruses_AssociationsFlatFile.csv b/clover/clover_0.1_mammalviruses/CLOVER_0.1_MammalViruses_AssociationsFlatFile.csv
diff --git a/clover/clover_1.0_allpathogens/CLOVER_1.0_Viruses_AssociationsFlatFile.csv b/clover/clover_1.0_allpathogens/CLOVER_1.0_Viruses_AssociationsFlatFile.csv
diff --git a/data/pathogennames_harmonised_rg/EID2_pathogendata_allpathogens_harmonised_20210407.csv b/data/pathogennames_harmonised_rg/EID2_pathogendata_allpathogens_harmonised_20210407.csv
@@ -5030,7 +5030,7 @@ human adenovirus d,human mastadenovirus d,human mastadenovirus d,virus,,,,,,,,,,
 human adenovirus e,human mastadenovirus e,human mastadenovirus e,virus,,,,,,,,,,,,,,,,
 human adenovirus f,human mastadenovirus f,human mastadenovirus f,virus,,,,,,,,,,,,,,,,
 human adenovirus g,human mastadenovirus g,human mastadenovirus g,virus,,,,,,,,,,,,,,,,
-human astrovirus,NA,NA,virus,,,,,,,,,,,,,,,,
+human astrovirus,human astrovirus,human astrovirus,virus,,,,,,,,,,,,,,,,
 human coronavirus 229e,human coronavirus 229e,human coronavirus 229e,virus,,,,,,,,,,,,,,,,
 human coronavirus hku1,human coronavirus hku1,human coronavirus hku1,virus,,,,,,,,,,,,,,,,
 human coronavirus nl63,human coronavirus nl63,human coronavirus nl63,virus,,,,,,,,,,,,,,,,

diff --git a/data/pathogennames_harmonised_rg/GMPD2_pathogendata_allpathogens_harmonised_20210407.csv b/data/pathogennames_harmonised_rg/GMPD2_pathogendata_allpathogens_harmonised_20210407.csv
@@ -1852,7 +1852,7 @@ tembusu,tembusu,tembusu virus,virus,0,0,0,0,0,0,NA,NA,0,0,NA,0,NA,0,,
 thiafora nairovirus,thiafora nairovirus,thiafora nairovirus,virus,0,0,0,0,0,0,NA,NA,0,0,NA,0,NA,0,,
 tick-borne encephalitis,tick-borne encephalitis,tick-borne encephalitis virus,virus,1,1,1,1,1,1,tick-borne encephalitis,"vector, food",1,1,tick (ixodes ricinus),1,tick-borne encephalitis,0,NA,NA
 uganda s,uganda s,uganda s virus,virus,0,0,0,0,0,0,NA,NA,0,0,NA,0,NA,0,,
-unassigned phocid gammaherpesvirus 2,NA,NA,virus,0,0,0,0,0,0,NA,NA,0,0,NA,0,NA,0,,
+unassigned phocid gammaherpesvirus 2,phocid gammaherpesvirus 2,phocid gammaherpesvirus 2,virus,0,0,0,0,0,0,NA,NA,0,0,NA,0,NA,0,,
 ungulate protoparvovirus 1,ungulate protoparvovirus 1,ungulate protoparvovirus 1,virus,0,0,0,0,0,0,NA,NA,0,0,NA,0,NA,0,,
 venezuelan equine encephalitis,venezuelan equine encephalitis,venezuelan equine encephalitis virus,virus,1,1,1,1,1,1,venezuelan equine encephalitis,vector,1,1,"mosquito (culex_spp,_aedes taeniorhynchus,_psorophora confinnis,_anopheles spp)",1,venezuelan equine encephalitis,1,NA,NA
 vesicular exanthema of swine,vesicular exanthema of swine,vesicular exanthema of swine virus,virus,0,0,0,0,0,0,NA,NA,0,0,NA,0,NA,0,,
@@ -1863,3 +1863,24 @@ yellow fever,yellow fever,yellow fever virus,virus,1,1,1,1,1,1,yellow fever,"vec
 zaire ebolavirus,zaire ebolavirus,zaire ebolavirus,virus,1,1,1,1,1,1,ebola,"direct, food",1,0,NA,1,ebola,1,NA,NA
 zika,zika,zika virus,virus,1,1,1,1,1,1,zika fever,"vector, sexual",1,1,mosquito (Aedes spp.),1,zika fever,1,NA,NA
 edwardsiella sp.,edwardsiella sp.,edwardsiella sp.,,1,1,0,0,1,0,NA,NA,0,0,NA,0,NA,1,,
+orthopoxvirus sp.,orthopoxvirus sp.,orthopoxvirus sp.,virus,,,,,,,,,,,,,,,,
+parapoxvirus sp.,parapoxvirus sp.,parapoxvirus sp.,virus,,,,,,,,,,,,,,,,
+flavivirus sp.,flavivirus sp.,flavivirus sp.,virus,,,,,,,,,,,,,,,,
+deltaretrovirus sp.,deltaretrovirus sp.,deltaretrovirus sp.,virus,,,,,,,,,,,,,,,,
+pestivirus sp.,pestivirus sp.,pestivirus sp.,virus,,,,,,,,,,,,,,,,
+cytomegalovirus sp.,cytomegalovirus sp.,cytomegalovirus sp.,virus,,,,,,,,,,,,,,,,
+lymphocryptovirus sp.,lymphocryptovirus sp.,lymphocryptovirus sp.,virus,,,,,,,,,,,,,,,,
+mastadenovirus sp.,mastadenovirus sp.,mastadenovirus sp.,virus,,,,,,,,,,,,,,,,
+rhadinovirus sp.,rhadinovirus sp.,rhadinovirus sp.,virus,,,,,,,,,,,,,,,,
+morbillivirus sp.,morbillivirus sp.,morbillivirus sp.,virus,,,,,,,,,,,,,,,,
+varicellovirus sp.,varicellovirus sp.,varicellovirus sp.,virus,,,,,,,,,,,,,,,,
+vesivirus sp.,vesivirus sp.,vesivirus sp.,virus,,,,,,,,,,,,,,,,
+parvovirus sp.,parvovirus sp.,parvovirus sp.,virus,,,,,,,,,,,,,,,,
+lentivirus sp.,lentivirus sp.,lentivirus sp.,virus,,,,,,,,,,,,,,,,
+enterovirus sp.,enterovirus sp.,enterovirus sp.,virus,,,,,,,,,,,,,,,,
+reovirus sp.,reovirus sp.,reovirus sp.,virus,,,,,,,,,,,,,,,,
+lyssavirus sp.,lyssavirus sp.,lyssavirus sp.,virus,,,,,,,,,,,,,,,,
+alphatorquevirus sp.,alphatorquevirus sp.,alphatorquevirus sp.,virus,,,,,,,,,,,,,,,,
+rotavirus sp.,rotavirus sp.,rotavirus sp.,virus,,,,,,,,,,,,,,,,
+alphavirus sp.,alphavirus sp.,alphavirus sp.,virus,,,,,,,,,,,,,,,,
+hantavirus sp.,hantavirus sp.,hantavirus sp.,virus,,,,,,,,,,,,,,,,
diff --git a/output/clover_metadata/CLOVER_HostParasite_ReportedNames.csv b/output/clover_metadata/CLOVER_HostParasite_ReportedNames.csv
diff --git a/output/clover_versions/CLOVER_Associations_Initial.csv b/output/clover_versions/CLOVER_Associations_Initial.csv
diff --git a/output/highertax_dict/paths_highertax.csv b/output/highertax_dict/paths_highertax.csv