tests/testthat/test-SangerContig-FASTA.R

In sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

### ============================================================================
### SangerContig ABIF Initial test
### ============================================================================
test_that("sangerContigFa Initial test", {
    expect_type(sangerContigFa, "S4")
    expect_s4_class(sangerContigFa, "SangerContig")
    expect_equal(sangerContigFa@inputSource, "FASTA")
    expect_equal(sangerContigFa@contigName, "Achl_ACHLO006-09")
    expect_equal(sangerContigFa@suffixForwardRegExp, "_[0-9]*_F")
    expect_equal(sangerContigFa@suffixReverseRegExp, "_[0-9]*_R")
    expect_equal(sangerContigFa@trimmingMethodSC, "")
    expect_equal(sangerContigFa@minReadsNum, 2)
    expect_equal(sangerContigFa@minReadLength, 20)
    expect_equal(sangerContigFa@refAminoAcidSeq, "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN")
    expect_equal(sangerContigFa@minFractionCall, 0.5)
    expect_equal(sangerContigFa@maxFractionLost, 0.5)
    expect_equal(sangerContigFa@acceptStopCodons, TRUE)
    expect_equal(sangerContigFa@readingFrame, 1)
    expect_equal(as.character(sangerContigFa@contigSeq), "TTATATTTTATTCTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGGATTACGTCTTGAACGAATTCCCCTGTTTGTCTGAGCTGTGCTAATTACAGTTGTTCTTCTACTTCTATCTTTACCAGTGCTAGCAGGTGCCATTACCATACTTCTTACCGACCGAAACCTCAATACTTCATTCTTTGATCCTGCCGGTGGTGGAGACCCCATCCTC")
    expect_equal(length(sangerContigFa@forwardReadList), 1)
    expect_equal(length(sangerContigFa@reverseReadList), 1)
})


### ============================================================================
### SangerContig Functions test
### ============================================================================
test_that("sangerContigFa - FASTA functions test -forward", {
    expect_message(updateQualityParam(sangerContigFa),
                   paste("SangerContig with 'FASTA' inputSource",
                         "cannot update quality parameters"))
})