GBQuickSearchFunc.R

# If you plan on using this code from the command line, check instead  GBQuickSearch.R

library("rentrez")

# For testing purposes
#   args<-"DQ061874"


gbq <- function(gbcode)
  {
  r<-entrez_summary(db="nuccore", id=gbcode)
  
  p<-entrez_link(dbfrom="nuccore", id=gbcode, db="all")
  
  pub<-p$links$nuccore_pubmed
  
  # Catch the exeption in case there is no connected article in pubmed
  if(is.null(pub)){
    pub= "No article found"
    
  } else {
    
    pub=paste('https://www.ncbi.nlm.nih.gov/pubmed/?term=',pub, sep="")
  }
  
  # link to the genebank entry
  
  gbl<-paste('https://www.ncbi.nlm.nih.gov/nuccore/', gbcode, sep="")
  
  pubm<-entrez_summary(db="pubmed", id=p$links$nuccore_pubmed)
  
  if(is.null(pubm)){
    pubm= 'No article found'
    
  }
  
  auth<-do.call(paste,pubm$authors[1])
  
  risultato <- cat('Title:', r$title, "\n", 'Organism: ', r$organism, "\n", 'PubMed: ', pubm$title, "\n", 'Authors: ', auth, "\n",pub, "\n", 'GenBank: ', gbl, "\n")
  
  output <- list(r, pubm, auth, pub, gbl)
  return(risultato)
  
}