tests/testthat/test-parse-iupac-extended.R

In glyparse: Parsing Glycan Structure Text Representations

test_that("monosaccharides are parsed correctly", {
  expect_mono <- function(iupac_ext, mono) {
    structure <- parse_iupac_extended(iupac_ext)
    graph <- glyrepr::get_structure_graphs(structure)
    expect_equal(igraph::V(graph)$mono, mono)
  }
  expect_mono("α-D-Glcp-(1→", "Glc")
  expect_mono("α-D-GlcpNAc-(1→", "GlcNAc")
  expect_mono("α-D-GlcpA-(1→", "GlcA")
  expect_mono("α-D-GlcpN-(1→", "GlcN")
  expect_mono("α-D-Neup5Ac-(2→", "Neu5Ac")
  expect_mono("α-D-Neup5Gc-(2→", "Neu5Gc")
  expect_mono("α-D-MurpN2Gc-(1→", "MurNGc")
  expect_mono("α-L-Eryp3CMeOH-(1→", "Api")
  expect_mono("L-gro-α-D-manHepp-(1→", "LDmanHep")
  expect_mono("D-gro-α-D-manHepp-(1→", "DDmanHep")
})

test_that("every furanose monosaccharide is parsed correctly", {
  furanose <- unname(furanose_monosaccharide_map())
  unusual_map <- unusual_configuration_monosaccharide_map()
  unusual_index <- match(furanose, unname(unusual_map))
  natural <- furanose
  natural[!is.na(unusual_index)] <- names(unusual_map)[
    unusual_index[!is.na(unusual_index)]
  ]
  unusual <- unname(unusual_map[natural])
  configuration <- invert_configuration(stringr::str_sub(unusual, 1, 1))
  configuration[!is.na(unusual_index)] <- stringr::str_sub(
    furanose[!is.na(unusual_index)],
    1,
    1
  )
  configuration[is.na(configuration)] <- "?"
  extended <- names(IUPAC_EXT_TO_CON)[match(natural, IUPAC_EXT_TO_CON)]
  anomer_pos <- glyrepr::get_anomer_pos(furanose)
  input <- paste0("?-", configuration, "-", extended, "-(", anomer_pos, "→")

  parsed <- parse_iupac_extended(input)
  graphs <- glyrepr::get_structure_graphs(parsed, return_list = TRUE)

  expect_identical(purrr::map_chr(graphs, ~ igraph::V(.x)$mono), furanose)
})


test_that("IUPAC-extended preserves unusual configurations", {
  parsed <- parse_iupac_extended(c(
    "α-L-Gulp-(1→",
    "β-D-Fucp3S-(1→",
    "?-D-Fucf-(1→"
  ))

  expect_identical(
    as.character(parsed),
    c("L-Gul(a1-", "D-Fuc3S(b1-", "D-Fucf(?1-")
  )
})


test_that("plain text format is parsed correctly", {
  expect_mono <- function(iupac_ext, mono) {
    structure <- parse_iupac_extended(iupac_ext)
    graph <- glyrepr::get_structure_graphs(structure)
    expect_equal(igraph::V(graph)$mono, mono)
  }
  expect_anomer <- function(iupac_ext, anomer) {
    structure <- parse_iupac_extended(iupac_ext)
    graph <- glyrepr::get_structure_graphs(structure)
    expect_equal(graph$anomer, anomer)
  }
  expect_linkage <- function(iupac_ext, linkage) {
    structure <- parse_iupac_extended(iupac_ext)
    graph <- glyrepr::get_structure_graphs(structure)
    expect_equal(igraph::E(graph)$linkage, linkage)
  }

  # Monosaccharides
  expect_mono("alpha-D-Glcp-(1->", "Glc")
  expect_mono("beta-D-Glcp-(1->", "Glc")
  expect_mono("alpha-D-GlcpNAc-(1->", "GlcNAc")

  # Anomers
  expect_anomer("alpha-D-Glcp-(1->", "a1")
  expect_anomer("beta-D-Glcp-(1->", "b1")

  # Linkages
  expect_linkage("alpha-D-Galp-(1->4)-beta-D-Galp-(1->", "a1-4")
  expect_linkage("beta-D-Galp-(1->4)-beta-D-Galp-(1->", "b1-4")
})


test_that("generic monosaccharides are parsed correctly", {
  expect_mono <- function(iupac_ext, mono) {
    structure <- parse_iupac_extended(iupac_ext)
    graph <- glyrepr::get_structure_graphs(structure)
    expect_equal(igraph::V(graph)$mono, mono)
  }
  expect_mono("α-?-Hexp-(1→", "Hex")
  expect_mono("α-?-HexpNAc-(1→", "HexNAc")
  expect_mono("α-?-HexpA-(1→", "HexA")
  expect_mono("α-?-HexpN-(1→", "HexN")
})


test_that("abbreviated generic reducing ends are parsed correctly", {
  parsed <- parse_iupac_extended(c("?-Hex", "?-HexNAc", "?-HexN"))

  expect_identical(
    as.character(parsed),
    c("Hex(?1-", "HexNAc(?1-", "HexN(?1-")
  )
})


test_that("substituents are parsed correctly", {
  expect_mono_and_sub <- function(iupac_ext, mono, sub) {
    structure <- parse_iupac_extended(iupac_ext)
    graph <- glyrepr::get_structure_graphs(structure)
    expect_equal(igraph::V(graph)$mono, mono)
    expect_equal(igraph::V(graph)$sub, sub)
  }
  expect_mono_and_sub("α-D-Glcp3Me-(1→", "Glc", "3Me")
  expect_mono_and_sub("α-D-GlcpNAc9Ac-(1→", "GlcNAc", "9Ac")
  expect_mono_and_sub("α-D-GlcpA2N-(1→", "GlcA", "2N")
  expect_mono_and_sub("α-D-Glcp?Me-(1→", "Glc", "?Me")
  expect_mono_and_sub("α-D-Glcp3Me6S-(1→", "Glc", "3Me,6S")
})


test_that("anomers are parsed correctly", {
  expect_anomer <- function(iupac_ext, anomer) {
    structure <- parse_iupac_extended(iupac_ext)
    graph <- glyrepr::get_structure_graphs(structure)
    expect_equal(graph$anomer, anomer)
  }
  expect_anomer("α-D-Glcp-(1→", "a1")
  expect_anomer("β-D-Glcp-(1→", "b1")
  expect_anomer("?-D-Glcp-(1→", "?1")
})


test_that("linkages are parsed correctly", {
  expect_linkage <- function(iupac_ext, linkage) {
    structure <- parse_iupac_extended(iupac_ext)
    graph <- glyrepr::get_structure_graphs(structure)
    expect_equal(igraph::E(graph)$linkage, linkage)
  }
  expect_linkage("α-D-Galp-(1→4)-β-D-Galp-(1→", "a1-4")
  expect_linkage("β-D-Galp-(1→4)-β-D-Galp-(1→", "b1-4")
  expect_linkage("?-D-Galp-(1→4)-β-D-Galp-(1→", "?1-4")
  expect_linkage("α-D-Galp-(1→?)-β-D-Galp-(1→", "a1-?")
  expect_linkage("α-D-Galp-(1→3/4)-β-D-Galp-(1→", "a1-3/4")
  expect_linkage("α-D-Galp-(1→4/?)-β-D-Galp-(1→", "a1-?")
})


test_that("parsing N-glycan core", {
  iupac <- "α-D-Manp-(1→3)[α-D-Manp-(1→6)]-β-D-Manp-(1→4)-β-D-GlcpNAc-(1→4)-β-D-GlcpNAc-(1→"
  expect_snapshot(parse_iupac_extended(iupac))
})