## ----setup, echo = FALSE--------------------------------------------------------------------------
knitr::opts_chunk$set(error = TRUE, cache = FALSE, eval = TRUE)
options(width = 100)

## -------------------------------------------------------------------------------------------------
library(biomaRt)

## ----test-wormbase-ssl, echo = FALSE, eval = FALSE------------------------------------------------
# if (
#   grepl(
#     try(httr::GET("https://parasite.wormbase.org"), silent = TRUE)[1],
#     pattern = "sslv3 alert handshake",
#     fixed = TRUE
#   )
# ) {
#   httr::set_config(httr::config(ssl_cipher_list = "DEFAULT@SECLEVEL=1"))
# }

## ----wormbase, echo=TRUE, eval=TRUE---------------------------------------------------------------
listMarts(host = "parasite.wormbase.org")
wormbase <- useMart(
  biomart = "parasite_mart",
  host = "https://parasite.wormbase.org",
  port = 443
)

## ----wormbase-2, echo=TRUE, eval=TRUE-------------------------------------------------------------
listDatasets(wormbase)
wormbase <- useDataset(mart = wormbase, dataset = "wbps_gene")
head(listFilters(wormbase))
head(listAttributes(wormbase))
getBM(
  attributes = c(
    "external_gene_id",
    "wbps_transcript_id",
    "transcript_biotype"
  ),
  filters = "gene_name",
  values = c("unc-26", "his-33"),
  mart = wormbase
)

## ----phytozome-13, echo = TRUE, eval = TRUE-------------------------------------------------------
phytozome_v13 <- useMart(
  biomart = "phytozome_mart",
  dataset = "phytozome",
  host = "https://phytozome-next.jgi.doe.gov"
)

## ----pytozome-2-----------------------------------------------------------------------------------
getBM(
  attributes = c("organism_name", "gene_name1"),
  filters = "gene_name_filter",
  values = "82092",
  mart = phytozome_v13
)

## ----sessionInfo----------------------------------------------------------------------------------
sessionInfo()
warnings()