## ----count_recs, echo=FALSE---------------------------------------------------
#are we on CRAN?
library(testthat)
build_this <- identical(Sys.getenv("BUILD_RENTREZ_VIGNETTE"), "true")

knitr::opts_chunk$set(eval = build_this) 


library(rentrez)
count_recs <- function(db, denom) {
    Sys.sleep(0.3)
    nrecs <-  rentrez::entrez_db_summary(db)["Count"]
    round(as.integer(nrecs)/denom, 1)
}

## ----dbs----------------------------------------------------------------------
# entrez_dbs()

## ----cdd----------------------------------------------------------------------
# entrez_db_summary("cdd")

## ----sra_eg-------------------------------------------------------------------
# entrez_db_searchable("sra")

## ----eg_search----------------------------------------------------------------
# r_search <- entrez_search(db="pubmed", term="R Language")

## ----print_search-------------------------------------------------------------
# r_search

## ----search_ids---------------------------------------------------------------
# r_search$ids

## ----searchids_2--------------------------------------------------------------
# another_r_search <- entrez_search(db="pubmed", term="R Language", retmax=40)
# another_r_search

## ----Tt-----------------------------------------------------------------------
# entrez_search(db="sra",
#               term="Tetrahymena thermophila[ORGN]",
#               retmax=0)

## ----Tt2----------------------------------------------------------------------
# entrez_search(db="sra",
#               term="Tetrahymena thermophila[ORGN] AND 2013:2015[PDAT]",
#               retmax=0)

## ----Tt3----------------------------------------------------------------------
# entrez_search(db="sra",
#               term="(Tetrahymena thermophila[ORGN] OR Tetrahymena borealis[ORGN]) AND 2013:2015[PDAT]",
#               retmax=0)

## ----sra_searchable-----------------------------------------------------------
# entrez_db_searchable("sra")

## ----mesh---------------------------------------------------------------------
# entrez_search(db   = "pubmed",
#               term = "(vivax malaria[MeSH]) AND (folic acid antagonists[MeSH])")

## ----connectome, fig.width=5, fig.height=4, fig.align='center'----------------
# search_year <- function(year, term){
#     query <- paste(term, "AND (", year, "[PDAT])")
#     entrez_search(db="pubmed", term=query, retmax=0)$count
# }
# 
# year <- 2008:2014
# papers <- sapply(year, search_year, term="Connectome", USE.NAMES=FALSE)
# 
# plot(year, papers, type='b', main="The Rise of the Connectome")

## ----elink0-------------------------------------------------------------------
# all_the_links <- entrez_link(dbfrom='gene', id=351, db='all')
# all_the_links

## ----elink_link---------------------------------------------------------------
# all_the_links$links

## ----elink_pmc----------------------------------------------------------------
# all_the_links$links$gene_pmc[1:10]

## ----elink_omim---------------------------------------------------------------
# all_the_links$links$gene_clinvar
# 

## ----elink1-------------------------------------------------------------------
# nuc_links <- entrez_link(dbfrom='gene', id=351, db='nuccore')
# nuc_links
# nuc_links$links

## ----elinik_refseqs-----------------------------------------------------------
# nuc_links$links$gene_nuccore_refseqrna

## ----outlinks-----------------------------------------------------------------
# paper_links <- entrez_link(dbfrom="pubmed", id=25500142, cmd="llinks")
# paper_links

## ----urls---------------------------------------------------------------------
# paper_links$linkouts

## ----just_urls----------------------------------------------------------------
# linkout_urls(paper_links)

## ----multi_default------------------------------------------------------------
# all_links_together  <- entrez_link(db="protein", dbfrom="gene", id=c("93100", "223646"))
# all_links_together
# all_links_together$links$gene_protein

## ----multi_byid---------------------------------------------------------------
# all_links_sep  <- entrez_link(db="protein", dbfrom="gene", id=c("93100", "223646"), by_id=TRUE)
# all_links_sep
# lapply(all_links_sep, function(x) x$links$gene_protein)

## ----Summ_1-------------------------------------------------------------------
# taxize_summ <- entrez_summary(db="pubmed", id=24555091)
# taxize_summ

## ----Summ_2-------------------------------------------------------------------
# taxize_summ$articleids

## ----Summ_3-------------------------------------------------------------------
# taxize_summ$pmcrefcount

## ----multi_summ---------------------------------------------------------------
# vivax_search <- entrez_search(db = "pubmed",
#                               term = "(vivax malaria[MeSH]) AND (folic acid antagonists[MeSH])")
# multi_summs <- entrez_summary(db="pubmed", id=vivax_search$ids)

## ----multi_summ2--------------------------------------------------------------
# extract_from_esummary(multi_summs, "fulljournalname")

## ----multi_summ3--------------------------------------------------------------
# date_and_cite <- extract_from_esummary(multi_summs, c("pubdate", "pmcrefcount",  "title"))
# knitr::kable(head(t(date_and_cite)), row.names=FALSE)

## ----transcript_ids-----------------------------------------------------------
# gene_ids <- c(351, 11647)
# linked_seq_ids <- entrez_link(dbfrom="gene", id=gene_ids, db="nuccore")
# linked_transripts <- linked_seq_ids$links$gene_nuccore_refseqrna
# head(linked_transripts)

## ----fetch_fasta--------------------------------------------------------------
# all_recs <- entrez_fetch(db="nuccore", id=linked_transripts, rettype="fasta")
# class(all_recs)
# nchar(all_recs)

## ----peak---------------------------------------------------------------------
# cat(strwrap(substr(all_recs, 1, 500)), sep="\n")

## ----Tt_tax-------------------------------------------------------------------
# Tt <- entrez_search(db="taxonomy", term="(Tetrahymena thermophila[ORGN]) AND Species[RANK]")
# tax_rec <- entrez_fetch(db="taxonomy", id=Tt$ids, rettype="xml", parsed=TRUE)
# class(tax_rec)

## ----Tt_list------------------------------------------------------------------
# tax_list <- XML::xmlToList(tax_rec)
# tax_list$Taxon$GeneticCode

## ----Tt_path------------------------------------------------------------------
# tt_lineage <- tax_rec["//LineageEx/Taxon/ScientificName"]
# tt_lineage[1:4]

## ----Tt_apply-----------------------------------------------------------------
# XML::xpathSApply(tax_rec, "//LineageEx/Taxon/ScientificName", XML::xmlValue)

## ----asthma-------------------------------------------------------------------
# upload <- entrez_post(db="omim", id=600807)
# upload

## ----snail_search-------------------------------------------------------------
# entrez_search(db="nuccore", term="COI[Gene] AND Gastropoda[ORGN]")

## ----snail_history------------------------------------------------------------
# snail_coi <- entrez_search(db="nuccore", term="COI[Gene] AND Gastropoda[ORGN]", use_history=TRUE)
# snail_coi
# snail_coi$web_history

## ----asthma_links-------------------------------------------------------------
# asthma_clinvar <- entrez_link(dbfrom="omim", db="clinvar", cmd="neighbor_history", id=600807)
# asthma_clinvar$web_histories

## ----asthma_links_upload------------------------------------------------------
# asthma_variants <- entrez_link(dbfrom="omim", db="clinvar", cmd="neighbor_history", web_history=upload)
# asthma_variants

## ----links--------------------------------------------------------------------
# snp_links <- entrez_link(dbfrom="clinvar", db="snp",
#                          web_history=asthma_variants$web_histories$omim_clinvar,
#                          cmd="neighbor_history")
# snp_summ <- entrez_summary(db="snp", web_history=snp_links$web_histories$clinvar_snp)
# knitr::kable(extract_from_esummary(snp_summ, c("chr", "fxn_class", "global_maf")))

## ----set_key------------------------------------------------------------------
# set_entrez_key("ABCD123")
# Sys.getenv("ENTREZ_KEY")