tests/testthat/test_findPatternPos.R

In alinaselega/BUMHMM: Computational pipeline for computing probability of modification from structure probing experiment data

# BUM-HMM
# Copyright (C) 2016 Alina Selega

context("Finding patterns in sequence")

sequence <- 'TGACGTG'

patterns <- nuclPerm(2)

test_that("function correctly finds patterns", {
    expect_equal(findPatternPos(patterns, sequence, '+')[[2]] == 3,
                 TRUE)
    expect_equal(all(findPatternPos(patterns, sequence, '+')[[15]]
                     == c(1, 6)), TRUE)
    expect_equal(
      is.na(findPatternPos(patterns, sequence, '+')[[1]]), TRUE)
})

test_that("function requires strand to be '+' or '-'", {
    expect_error(findPatternPos(patterns, sequence, 'plus'),
              "Strand should be either plus or minus, specified with a sign.")
})

test_that("function requires a non-empty sequence", {
    expect_error(findPatternPos(patterns, '', '+'),
                 "The sequence should be non-empty.")
})

test_that("function requires a non-empty list of patterns", {
    expect_error(findPatternPos(list(), sequence, '+'),
                 "The list of patterns should be non-empty.")
})