tests/testthat/test_align.R

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

context("Perform multiple sequence alignment")
library(LymphoSeq2)
library(tidyverse)

test_that("Align all sequences in all sample within edit distance of 15", {
  base::set.seed(12357)
  stable <- LymphoSeq2::readImmunoSeq("test_data/", threads = 1)
  ntable <- LymphoSeq2::productiveSeq(stable, aggregate = "junction")
  nalign <- LymphoSeq2::alignSeq(ntable)
  nseq <- base::length(nalign@unmasked)
  known_consensus <- "---------------?T??A??CC?C?GAGC??G??GACTC?GCC?TGTATCTCTGTGCCAGCAGC???G????????????????????????---------?????T??TT?GG????------"
  test_consensus <- suppressMessages(msa::msaConsensusSequence(nalign))
  expect_equal(nseq, 600)
})

test_that("Align all sequences in one sample within edit distance of 15", {
  ttable <- LymphoSeq2::readImmunoSeq("test_data/", threads = 1)
  tntable <- LymphoSeq2::productiveSeq(ttable, aggregate = "junction")
  talign <- LymphoSeq2::alignSeq(tntable, repertoire_ids = "015V12001549_CFAR")
  tseq <- base::length(talign@unmasked)
  tconsensus <- suppressMessages(msa::msaConsensusSequence(talign))
  tname <- base::unique(stringr::str_remove(base::names(talign@unmasked), "_\\d+"))
  ktable <- LymphoSeq2::readImmunoSeq("test_data/015V12001549_CFAR.tsv", threads = 1)
  kntable <- LymphoSeq2::productiveSeq(ktable, aggregate = "junction")
  kalign <- LymphoSeq2::alignSeq(kntable)
  kseq <- base::length(kalign@unmasked)
  kconsensus <- suppressMessages(msa::msaConsensusSequence(kalign))
  kname <- "015V12001549_CFAR"
  expect_equal(tconsensus, kconsensus)
  expect_equal(tseq, kseq)
  expect_equal(tname, kname)
})

test_that("Align single sequence in all samples within edit distance of 15", {
  base::set.seed(12357)
  ttable <- LymphoSeq2::readImmunoSeq("test_data/", threads = 1)
  tntable <- LymphoSeq2::productiveSeq(ttable, aggregate = "junction")
  talign <- LymphoSeq2::alignSeq(tntable, sequence_list = c("AATTCCCTGGAGCTTGGTGACTCTGCTGTGTATTTCTGTGCCAGCAGCTATAGAGCGGGGGCTGGCGGTGAGCAGTTCTTCGGGCCA"))
  tseq <- base::length(talign@unmasked)
  tconsensus <- suppressMessages(msa::msaConsensusSequence(talign))
  tname <- length(base::unique(stringr::str_remove(base::names(talign@unmasked), "_\\d+")))
  kseq <- 20
  kconsensus <- "------ATCAATTCCCTGGAGCTTGGTGACTCTGCTGTGTATTTCTGTGCCAGCAGCCAAG??GG?GGGG?G?AC?A??AG?AGTTCTTCGGGC??---"
  kname <- 4
  expect_equal(tconsensus, kconsensus)
  expect_equal(tseq, kseq)
  expect_equal(tname, kname)
})