DArT (well a modified DArT) to Flapjack format.

Input file (tab delimited text file but an easy tweak in the code to change to csv) needs to be in this form.

Allele_ID,snp,266759,194916,195959,191884,191481,206877,207069

1002968|F|0--60:C>T,60:C>T,0,1,1,1,0,1,0

1002968|F|0--60:C>T-60:C>T,60:C>T,1,0,1,0,1,0,1

The calls will be in pairs of lines, these should be sequential in the file.

Outputs this format

DArT Marker Name/Line 266759 194916 195959 191884 191481 206877 207069

1002968|F|0--60:C>T T C C/T C T C T

The encoding is based on:
Allele CT

01  -> TT (i.e., homozygote for T)

-1  -> ?T (i.e., homozygote for T or heterozygote)

10  -> CC (i.e., homozygote for C)

1-  -> C? (i.e., homozygote for C or heterozygote)

11  -> CT (i.e., heterozygote)

This is Perl code. Requires input file in $ARGV[0] and output in $ARGV[1] which are passed as command line arguments as you would expect.

So to run this script you need Perl installed then...

perl dart_to_matrix.pl inputfile.in outputfile.out