tests/testthat/helper-SangerAlignment-ABIF.R

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

rawDataDir <- system.file("extdata", package = "sangeranalyseR")
parentDir <- file.path(rawDataDir, "Allolobophora_chlorotica", "ACHLO")
suffixForwardRegExp <- "_[0-9]*_F.ab1"
suffixReverseRegExp <- "_[0-9]*_R.ab1"
sangerAlignment <- new("SangerAlignment",
                       inputSource           = "ABIF",
                       processMethod         = "REGEX",
                       ABIF_Directory       = parentDir,
                       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)