The point is that I would like to have a single sequence (for each individual) where heterozygous positions should be coded according to the IUPAC nucleotide ambiguity codes.
Input example (.ped)
AUT-DBA 1 0 0 0 -9 C C C C G C G G
AUT-DBA 2 0 0 0 -9 C C C C C A G G
Expected output (fasta code)
>AUT-DBA 1
CCSG
>AUT-DBA 2
CCMG
Stefano Capomaccio
I attach the file I sent you for other scientists.
The script is written in perl.
Launch as follows
perl ped_to_iupac_onestep.txt example.ped > fasta.results
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Stefano Capomaccio
Please use the version attached here, the other will produce shorten sequences if there are missing coded as 00.
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