## need locus tags from GFF file values(bpgff)$locus
## avoid V. cholerae strain tags... VC274080_0898 or VC0395_A2856?
## tag <- paste(prefix, "[0-9]{4}[^0-9_]", sep="")
# or Helicobacter strain j99 tags -- HP not JHP_
# txt should be list returned by pmcText or table
findTags <-function(txt, tags, prefix, suffix, notStartingWith, expand=TRUE, digits=4, ...){
id <- attr(txt, "id")
if(is.null(id)){
if(is.list(txt)) id <- attr(txt[[1]], "id") # list of tables
if(is.null(id)){
message("Warning: No id attribute found")
id <- NA
}
}
## one or more digits
tag <- paste(prefix, "[0-9]+", sep="")
y <- searchPMC(txt, tag, ...)
if(!is.null(y)){
message(paste(nrow(y), "matches"))
y <- parseTags(y, tags, prefix, suffix, notStartingWith, expand, digits )
## may not extract any tags if using notStartingWith
if(nrow(y) == 0){
y <- NULL
}else{
## add ID
y <- data.frame(id, y, stringsAsFactors=FALSE)
}
}
y
}
#
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