tests/testthat/test-tools-sqs.R

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

# LIBS
library(phylotaR)
library(testthat)

# DATA
# from the wild
raw_recs <- readRDS(phylotaR:::datadir_get("raw_seqrecs.rda"))
# selected to represent record diversity
test_raw_recs <- readRDS(phylotaR:::datadir_get("raw_seqrecs2.rda"))
wd <- tempdir()
ps <- parameters(wd = wd)

# RUNNING
context("Testing 'tools-sqs'")
test_that("gb_extract() works", {
  for (test_raw_rec in test_raw_recs) {
    record_parts <- phylotaR:::gb_extract(record = test_raw_rec)
    test <- names(record_parts) %in% c(
      "accession", "version", "definition",
      "sequence", "moltype", "features",
      "date", "organism", "keywords"
    )
    expect_true(all(test))
  }
})
test_that("rawseqrec_breakdown() works", {
  for (test_raw_rec in test_raw_recs) {
    record_parts <- phylotaR:::gb_extract(record = test_raw_rec)
    seqrecs <- phylotaR:::rawseqrec_breakdown(
      record_parts = record_parts,
      ps = ps
    )
    expect_true(inherits(seqrecs[[1]], "SeqRec"))
  }
})
test_that("seqrec_convert() works", {
  for (raw_rec in raw_recs) {
    sqs <- phylotaR:::seqrec_convert(raw_recs = raw_rec, ps = ps)
    expect_true(inherits(sqs[[1]], "SeqRec"))
  }
})
test_that("seqrec_gen() works", {
  seqrec <- phylotaR:::seqrec_gen(
    accssn = "1", nm = "1", txid = "1",
    sq = "atcg", dfln = "defline",
    orgnsm = "G. sp", ml_typ = "DNA",
    rec_typ = "Full", vrsn = "1.1",
    age = 30L
  )
  expect_true(inherits(seqrec, "SeqRec"))
})
test_that("seqarc_gen() works", {
  seqrec1 <- phylotaR:::seqrec_gen(
    accssn = "1", nm = "1", txid = "1",
    sq = "atcg", dfln = "defline",
    orgnsm = "G. sp", ml_typ = "DNA",
    rec_typ = "Full", vrsn = "1.1",
    age = 30L
  )
  seqrec2 <- phylotaR:::seqrec_gen(
    accssn = "2", nm = "1", txid = "1",
    sq = "atcg", dfln = "defline",
    orgnsm = "G. sp", ml_typ = "DNA",
    rec_typ = "Full", vrsn = "2.1",
    age = 30L
  )
  seqarc <- phylotaR:::seqarc_gen(seqrecs = list(seqrec1, seqrec2))
  expect_true(inherits(seqarc, "SeqArc"))
})

# # Example raw_recs ----
# term <- phylotaR:::searchterm_gen(txid = '2759', ps = parameters(),
#                                   direct = FALSE)
# search_obj <- rentrez::entrez_search(db = 'nucleotide', term = term,
#                                      retmax = 0, use_history = TRUE)
# # random 100 sequences
# retmaxes <- round(runif(n = 100, min = 1, max = search_obj[['count']]))
# raw_recs <- NULL
# for (i in retmaxes) {
#   print(i)
#   whobj <- search_obj[['web_history']]
#   raw_rec <- rentrez::entrez_fetch(db = 'nucleotide', retstart = i,
#                                    retmode = 'text', rettype = 'gb',
#                                    web_history = whobj,
#                                    retmax = sample(1:4, 1))
#   raw_recs <- c(raw_recs, raw_rec)
# }
# otfl <- phylotaR:::datadir_get('raw_seqrecs.rda')
# saveRDS(object = raw_recs, file = otfl)