tests/testthat/helper-SangerContig-ABIF.R

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

inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")
inputFilesParentDir <- file.path(inputFilesPath, "Allolobophora_chlorotica", "ACHLO")
contigName <- "Achl_ACHLO006-09"
suffixForwardRegExp <- "_[0-9]*_F.ab1"
suffixReverseRegExp <- "_[0-9]*_R.ab1"
sangerContig <- new("SangerContig",
                    inputSource           = "ABIF",
                    processMethod         = "REGEX",
                    ABIF_Directory       = inputFilesParentDir,
                    contigName            = contigName,
                    REGEX_SuffixForward   = suffixForwardRegExp,
                    REGEX_SuffixReverse   = suffixReverseRegExp,
                    refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN",
                    TrimmingMethod        = "M1",
                    M1TrimmingCutoff      = 0.0001,
                    M2CutoffQualityScore  = NULL,
                    M2SlidingWindowSize   = NULL,
                    baseNumPerRow         = 100,
                    heightPerRow          = 200,
                    signalRatioCutoff     = 0.33,
                    showTrimmed           = TRUE,
                    processorsNum         = 2)

inputFilesParentDir2 <- file.path(inputFilesPath, "Allolobophora_chlorotica", "RBNII")
contigName2 <- "Achl_RBNII384-13"

sangerContig2 <- new("SangerContig",
                    inputSource           = "ABIF",
                    processMethod         = "REGEX",
                    ABIF_Directory       = inputFilesParentDir2,
                    contigName            = contigName2,
                    REGEX_SuffixForward   = suffixForwardRegExp,
                    REGEX_SuffixReverse   = suffixReverseRegExp,
                    refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN",
                    TrimmingMethod        = "M1",
                    M1TrimmingCutoff      = 0.0001,
                    M2CutoffQualityScore  = NULL,
                    M2SlidingWindowSize   = NULL,
                    baseNumPerRow         = 100,
                    heightPerRow          = 200,
                    signalRatioCutoff     = 0.33,
                    showTrimmed           = TRUE,
                    processorsNum         = 2)