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Changing To Reverse Complementary Snp Nucleotides

Hello everyone, I would like to change allele codes to the reverse complement, this is the file that I have, is composed of Allele 1, Allele2 and Strand Orientation:

A    T    +
T    T    +
A    T    - 
C    T    -
G    G    -
G    C    +
A    G    -

I need to flip only the ones oriented to the minus strand, so the result would be like this:

A    T    +
T    T    +
T    A    +
G    A    +
C    C    +
G    C    +
T    C    +

The file is tab separated and has arround 580k SNPs, I will really appreciate if you can help me with some nice awk/perl or any code to do that :)

snp
• 4,270 views • link
updated by JC JC • written by bibb77 bibb77

3 answers

POL:

perl -pe 'tr/ACGT-/TGCA+/ if (/-/)' < SNP.list > SNP.for
• 164 views • link
written by JC JC 
 sed 's/\(.\)\t\(.\)\t\-$/\2\t\1\t+/' < input.txt
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks. I don't know if I'm missing something but I applied your code to my input and it doesn't result like the given output file.

• 0 views • link
written by bibb77 bibb77

Maybe some awk:

BEGIN{OFS="\t"}
function complement (nuc) {
    switch (nuc) {
        case /[aA]/:
            return "T"
        case /[tT]/:
            return "A"
        case /[cC]/:
            return "G"
        case /[gG]/:
            return "C"
        default:
            return "N"
    }
}

$3 != "-" {print $1, $2, $3}
$3 == "-" {print complement($1), complement($2), "+"}

Saved to a file complement_alleles.awk and run with:

awk -f complement_alleles.awk < input.txt
• 0 views • link
written by Rob Syme Rob Syme

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