README.md

ima2arlequin

These scripts are used to convert the *.ima file created by rad_haplotyper and convert it to arlequin.

pgdspider fails when trying to convert these files, which are ima2 formatted

How To

There is hardcoding in these scripts that you will have to adjust to work for your specific files.

# split ima file into 2 almost tidy files that can be read by the R script
bash ima2arlequin_files.bash

Run the ima2arlequin.R script. I made this in Rstudio and have not made it commandline friendly

# run the next bash file which converts the output from the R script to be closer to arlequin format
bash ima2arlequin_afterR.bash

I manually copied and pasted the population specific haplotype data to an arelquin file that was made with pgdspider using the genepop output from rad_haplotyper

While you are manually editing that arlequin file, don't forget to rename it and make sure the header is correct.

[Profile]
  Title = "MyRadHapOut.haps.genepop"
  NbSamples = 5
  DataType = DNA
  GenotypicData = 1
  LocusSeparator = WHITESPACE
  MissingData = "?"
  GameticPhase = 0
  RecessiveData = 0

# remove the tidy formated population identifiers from each pop (you will need to modify the code for your popnames)
bash ima2arlequin_aftermanualcopypaste.bash

Finally add a structure block onto the end of the arlquin file. It must include all of your pops

[[Structure]]
	StructureName = "One cluster"
	NbGroups = 1

	Group = {
		"At_Sk"
		"At_Mk"
		"Pk"
		"St"
		"Kr"
	}