## This code is part of the megaptera package
## © C. Heibl 2014 (last update 2019-10-30)
dbExcludeIndet <- function(x){
## PARAMETERS
## -----------
gene <- x@locus@sql
acc.tab <- paste("acc", gsub("^_", "", gene), sep = "_")
indet <- c("_sp[.]?([_-]|$)", # Amanita_sp Amanita_sp. Amanita_sp_xxx Amanita_sp._xxx Amanita_sp-53
"spec$",
"_cf[.]",
"_aff[.]",
"hybrid$",
"Group$",
"cultivar$",
"environmental", # environmental_sample
"^fungal",
"uncultured",
"unknown",
".[[:upper:]]",
"^[[:lower:]]")
if (x@taxon@exclude.hybrids){
indet <- union(indet, "_x_|^x_")
}
indet <- paste(indet, collapse = "|")
conn <- dbconnect(x@db)
indet <- paste("UPDATE", acc.tab,
"SET status = 'excluded (indet)'",
"WHERE", wrapSQL(indet, term = "spec_ncbi",
boolean = NULL))
dbSendQuery(conn, indet)
# singles quotes are escaped by single quotes in pgSQL!
dbSendQuery(conn, paste("UPDATE", acc.tab,
"SET status = 'excluded (indet)'",
"WHERE spec_ncbi~''''"))
dbDisconnect(conn)
}
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