Look at the fasta file, these files came straight out of the stacks pipeline,
I can get the pipeline, if you need it.
then execute 

for Peter Beerli's stacks2migrate.py use:

cat example.fasta | python stacks2mig.py 
or
python stacks2migrate.py -i stacksfile.fa -o infile

help:
syntax: python stacks2mig.py < -i stacksfile.fa >  <-o migratefile> <-r> <-l>
<> means options
 -i filename # expects a stacks fasta file, if ommited reads from standard input
 -o filename # outputfilename to write the migrate infile to, if omitted writes to standard out
 -r          # removes trailing 'N', if omitted does not remove trailing 'N'
 -l          # interactively asks about reordering the locations in the outputfile
 The title for each sequence in the fasta file must look like this:
 >CLocus_12706_Sample_1_Locus_34105_Allele_0 [BayOfIslands_s088.fq; groupI, 125578, +]
         xxxxx                             x  xxxxxxxxxxxx xxxx
 where the xxx are extracted for the conversion
 The sequence must be on one line!

 MIT license, Peter Beerli 2025



this will generate a migrate infile


for Paul Maier's fasta2genotype.py you will need additional files
I made an attempt to move it from python 2 to Python 3 but this is unfinished.


