tests/test_chksum.R

In seguid: Sequence Globally Unique Identifier (SEGUID) Checksums

library(seguid)

reverse <- seguid:::reverse

assert_error <- function(expr, envir = parent.frame()) {
  expr <- substitute(expr)
  res <- tryCatch(eval(expr, envir = envir), error = identity)
  if (!inherits(res, "error")) {
    stop("Call did not result in an error: ", deparse(expr))
  }
}


stopifnot(  seguid("AT") ==   "seguid=Ax/RG6hzSrMEEWoCO1IWMGska+4")
stopifnot(lsseguid("AT") == "lsseguid=Ax_RG6hzSrMEEWoCO1IWMGska-4")

NP_313053_1 <- paste0(
  "MKALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSG",
  "ASRGIRLLQEEEEGLPLVGRVAAGEPLLAQQHIEGHYQVDPSLFKPNADFLLRVSGMSMKD",
  "IGIMDGDLLAVHKTQDVRNGQVVVARIDDEVTVKRLKKQGNKVELLPENSEFKPIVVDLRQ",
  "QSFTIEGLAVGVIRNGDWL"
)
#stopifnot(seguid(NP_313053_1, alphabet="{DNA-extended}") == "seguid=2c4yjE+JqjvzYF1d0OmUh8pCpz8")


m13dna <- readLines("test_data/M13.txt")
truth <- "csseguid=aAjgnsF9cPI6cu8IQ81sYnstVzU"
stopifnot(csseguid(m13dna) == truth)


truth <- "ldseguid=odgytmQKSOnFEUorGIWK3NDjqUA"
stopifnot(ldseguid("AT", "AT") == truth)

truth <- "ldseguid=-9xkp3UfucL4bSPxYODh8i9KFEE"
stopifnot(ldseguid("-AT", "-TA") == truth)

truth <- "ldseguid=-9xkp3UfucL4bSPxYODh8i9KFEE"
stopifnot(ldseguid("-TA", "-AT") == truth)

truth <- "ldseguid=ToSxUXWMCIKz-FYdXJ3Qq-bS_8o"
stopifnot(ldseguid("CTATAG", "--AT--") == truth)
stopifnot(ldseguid("--AT--", "CTATAG") == truth)

truth <- "cdseguid=5fHMG19IbYxn7Yr7_sOCkvaaw7U"
stopifnot(cdseguid("ACGTT", "AACGT") == truth)
stopifnot(cdseguid("AACGT", "ACGTT") == truth)

pUC19dna <- readLines("test_data/pUC19.txt", warn = FALSE)
pUC19dna_rc <- reverse(chartr("ACGT", "TGCA", pUC19dna))
truth <- "cdseguid=mCC0B3UMZfgLyh3Pl574MVjm30U"
stopifnot(cdseguid(pUC19dna, pUC19dna_rc) == truth)
bfr <- readLines("test_data/pUC19_minimal_rotation_watson_linebreak_crick.txt", warn = FALSE)
w <- bfr[1]
c <- bfr[2]
stopifnot(ldseguid(w, reverse(c)) == gsub("cdseguid=", "ldseguid=", truth))


## Empty input is considered an error
assert_error(seguid::seguid(""))
assert_error(seguid::lsseguid(""))
assert_error(seguid::csseguid(""))
assert_error(seguid::cdseguid("", ""))



## Use checksums as filenames
seq <- "GATTACA"
## Comment:
## The   SEGUID check is seguid=tp2jzeCM2e3W4yxtrrx09CMKa/8
## The slSEGUID check is seguid=tp2jzeCM2e3W4yxtrrx09CMKa_8
td <- tempdir()
filename <- seguid::lsseguid(seq)
pathname <- file.path(td, filename)
cat(seq, file = pathname)
stopifnot(utils::file_test("-f", pathname))
content <- readLines(pathname, warn = FALSE)
stopifnot(identical(content, seq))
file.remove(pathname)
unlink(td)