Issues with Reproducible tutorial

jspychalla commented 1 year ago

Hello,

I am trying to run the reproducible example from :

When I run the SangerAlignment function below

my_sangerAlignment <- new("SangerAlignment", inputSource = "ABIF", processMethod = "REGEX", ABIF_Directory = parentDir, REGEXSuffixForward = "[0-9]_F.ab1$", REGEXSuffixReverse = "[0-9]_R.ab1$", TrimmingMethod = "M1", M1TrimmingCutoff = 0.0001, M2CutoffQualityScore = NULL, M2SlidingWindowSize = NULL, baseNumPerRow = 100, heightPerRow = 200, signalRatioCutoff = 0.33, showTrimmed = TRUE, refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN", minReadsNum = 2, minReadLength = 20, minFractionCall = 0.5, maxFractionLost = 0.5, geneticCode = GENETIC_CODE, acceptStopCodons = TRUE, readingFrame = 1, processorsNum = 2)

I get the following error message:

Error in IdClusters(dist, type = "both", showPlot = FALSE, processors = processorsNum, : unused arguments (type = "both", showPlot = FALSE)

This same error appears when I run

rawDataDir <- system.file("extdata", package = "sangeranalyseR") parentDir <- file.path(rawDataDir, 'Allolobophora_chlorotica', 'ACHLO')

ACHLO_contigs <- SangerAlignment(ABIF_Directory = parentDir, REGEXSuffixForward = "[0-9]_F.ab1$", REGEXSuffixReverse = "[0-9]_R.ab1$")

The version of R I am working in is 4.2.2.

jspychalla commented 1 year ago

I realize that the SangerAlignment function is not present even though I have the package loaded. Is there a way to fix this? Thank you :)

Kuanhao-Chao commented 1 year ago

Hi @jspychalla,

Please excuse the delay.

DECIPHER changed the IdClusters function to TreeLine. But this issue was solved in 3.15 release. Which version of sangeranalyseR are you using?

Please upgrade it by running

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("sangeranalyseR")

And you still cannot load the function, please send me an email to kuanhao.chao@gmail.com

Best, Kuan-Hao

roblanf / sangeranalyseR

Issues with Reproducible tutorial #85