tests/testthat/helper-SangerRead-prechecking.R

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

inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")
# 1. FILE_NOT_EXISTS_ERROR
SRab1_File_Not_Exist_Error <- file.path(inputFilesPath,
                                        "Allolobophora_chlorotica",
                                        "ACHLO",
                                        "TEST_Achl_ACHLO006-09_2_R.ab1")
sangerReadR_File_Not_Exist_Error <- new("SangerRead",
                                        readFeature           = "Reverse Read",
                                        readFileName          = SRab1_File_Not_Exist_Error,
                                        geneticCode           = GENETIC_CODE,
                                        TrimmingMethod        = "M1",
                                        M1TrimmingCutoff      = 0.0001,
                                        M2CutoffQualityScore  = NULL,
                                        M2SlidingWindowSize   = NULL,
                                        baseNumPerRow         = 100,
                                        heightPerRow          = 200,
                                        signalRatioCutoff     = 0.33,
                                        showTrimmed           = TRUE)


# # 2. FILE_TYPE_ERROR: ab1 file
# SRab1_FILE_TYPE_ERROR <- file.path(inputFilesPath,
#                                    "Allolobophora_chlorotica",
#                                    "ACHLO",
#                                    "Achl_ACHLO006-09_1_F.ab2")
# sangerReadF_FILE_TYPE_ERROR <- new("SangerRead",
#                                    readFeature           = "Forward Read",
#                                    readFileName          = SRab1_FILE_TYPE_ERROR,
#                                    geneticCode           = GENETIC_CODE,
#                                    TrimmingMethod        = "M1",
#                                    M1TrimmingCutoff      = 0.0001,
#                                    M2CutoffQualityScore  = NULL,
#                                    M2SlidingWindowSize   = NULL,
#                                    baseNumPerRow         = 100,
#                                    heightPerRow          = 200,
#                                    signalRatioCutoff     = 0.33,
#                                    showTrimmed           = TRUE)
# 
# # 3. FILE_TYPE_ERROR: fasta file
# SRfa_FILE_TYPE_ERROR <- file.path(inputFilesPath,
#                                   "fasta",
#                                   "SangerRead",
#                                   "Achl_ACHLO006-09_1_F.fast")
# sangerReadF_FILE_TYPE_ERROR <- new("SangerRead",
#                                    readFeature           = "Forward Read",
#                                    inputSource           = "FASTA",
#                                    readFileName          = SRfa_FILE_TYPE_ERROR,
#                                    geneticCode           = GENETIC_CODE,
#                                    TrimmingMethod        = "M1",
#                                    M1TrimmingCutoff      = 0.0001,
#                                    M2CutoffQualityScore  = NULL,
#                                    M2SlidingWindowSize   = NULL,
#                                    baseNumPerRow         = 100,
#                                    heightPerRow          = 200,
#                                    signalRatioCutoff     = 0.33,
#                                    showTrimmed           = TRUE)