read_PubMedRec <- function(PMIDfile, rettype){
recFile <- list()
pubmedF <- readLines(PMIDfile, n=-1L, warn=FALSE)
if (rettype=="docsum"){
gLins <- grep("^[0-9]*: ", pubmedF)
for (i in 1:length(gLins)){
ifelse (gLins[i]==gLins[length(gLins)], m <- length(pubmedF), m <- gLins[i + 1])
recFile[[i]] <- list()
recFile[[i]]$FullRecord <- sub(" *[0-9]*: ", "", paste(pubmedF[gLins[[i]]:(m-1)], collapse=" "), "[.] ")
recFile[[i]]$PMID <- sub("[.]", "", rev(grep("[0-9]*[.]", strsplit(sub(" *[0-9]*: ", "", paste(pubmedF[gLins[[i]]:(m-1)], collapse=" "), "[.] "), " ")[[1]],value = TRUE))[[1]])
if (length(grep("doi:", recFile[[i]]$FullRecord))==0){
recFile[[i]]$doi <- "No DOI"
}
else{
recFile[[i]]$doi <- sub("[.] .*", "", sub(".*doi: ", "", recFile[[i]]$FullRecord))
}
}
}
else if (rettype=="abstract"){
gLins <- grep("^[0-9]*[.] ", pubmedF)
for (i in 1:length(gLins)){
recFile[[i]] <- list()
if (i==length(gLins)){
m <- length(pubmedF)
recFile[[i]]$FullRecord <- paste(pubmedF[gLins[[i]]:m], sep="\n", collapse="\n")
recFile[[i]]$doi <- sub(" ", "", sub("^DOI: ", "", grep("DOI: ", pubmedF[gLins[[i]]:m], value = TRUE)))
recFile[[i]]$PMID <- sub(" ", "", sub(" *\\[.*\\]", "", sub("^PMID: ", "", grep("PMID: ", pubmedF[gLins[[i]]:m], value = TRUE))))
}
else if (i<length(gLins)){
m <- i + 1
recFile[[i]]$FullRecord <- paste(pubmedF[gLins[[i]]:(gLins[[m]]-1)], sep="\n", collapse="\n")
recFile[[i]]$doi <- sub(" ", "", sub("^DOI: ", "", grep("DOI: ", pubmedF[gLins[[i]]:(gLins[[m]]-1)], value = TRUE)))
recFile[[i]]$PMID <- sub(" ", "", sub(" *\\[.*\\]", "", sub("^PMID: ", "", grep("PMID: ", pubmedF[gLins[[i]]:(gLins[[m]]-1)], value = TRUE))))
}
}
}
recFile <- unlist(recFile, recursive=FALSE)
recFile
}
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