Padded position in Consensus sequence

Discussion in 'Perl Misc' started by Jayaprakash Rudraraju, Aug 14, 2003.

  1. Hi,

    I have written a small subroutine to as part of the program to tag primers
    in Consed. The following subroutine gives padded position on the consensus
    sequence, given its position on reference sequence.

    #!perl -w
    my $consensus = "AGG*TGAC**TA***AGTCCT*T";
    print map { "$_\t". padded_position($_) ."\n"} (1..16);

    sub padded_position {
    my ($unpad, $pads) = (@_, 0);
    $pads++ until $unpad == substr($consensus, 0, $unpad+$pads) =~ tr/ACGT//;

    can you suggest me some more efficient or elegant solutions. Eventhough I
    have condensed it as much as I can, I am looking for a simpler logic.

    Jayaprakash Rudraraju, Aug 14, 2003
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