tests/testthat/test-CRAN-optional-groups.R

In namedCapture: Named Capture Regular Expressions

library(testthat)
library(namedCapture)
context("optional groups")
source(system.file("test_engines.R", package="namedCapture", mustWork=TRUE), local=TRUE)

subject <- c(
  ten="chr10:213,054,000-213,055,000",
  M="chrM:111,000-222,000",
  no.match="foo bar",
  missing=NA,
  two="chr1:110-111 chr2:220-222",
  no.end="chr1:110 chr2:220-222")

pattern <- paste0(
  "(?P<chrom>chr[^:]+)",
  ":",
  "(?P<chromStart>[^- ]+)",
  "(?:",
  "-",
  "(?P<chromEnd>[^ ]+)",
  ")?")

test_engines("match one optional group", {
  computed.mat <- str_match_named(subject, pattern)
  expected.mat <- cbind(
    chrom=c("chr10", "chrM", NA, NA, "chr1", "chr1"),
    chromStart=c("213,054,000", "111,000", NA, NA, "110", "110"),
    chromEnd=c("213,055,000", "222,000", NA, NA, "111", ""))
  rownames(expected.mat) <- names(subject)
  expect_identical(computed.mat, expected.mat)
})

test_engines("match all optional groups", {
  computed.list <- str_match_all_named(subject, pattern)
  expected.list <- list(
    ten=cbind(chrom="chr10", chromStart="213,054,000", chromEnd="213,055,000"),
    M=cbind(chrom="chrM", chromStart="111,000", chromEnd="222,000"),
    no.match=matrix(character(), nrow=0),
    missing=matrix(character(), nrow=0),
    two=cbind(chrom=c("chr1", "chr2"),
              chromStart=c("110", "220"),
              chromEnd=c("111", "222")),
    no.end=cbind(chrom=c("chr1", "chr2"),
                 chromStart=c("110", "220"),
                 chromEnd=c("", "222")))
  expect_identical(computed.list, expected.list)
})