Hello Monks... I have a gene that is present in the genome in reverse complement, but the SNPs were described as though it was in standard 5' to 3' format. I'm trying to write a script that will change instances of "A" "C" "G" "T" in a tab delimited txt infile (from Excel) into "T" "G" "C" "A" in an output file while keeping the first column (the rows identifying all of the samples) and column headers (identifying all positions where SNPs occur) the same... I've not been very successful... here's what I have. Please bear with me as I'm very new to programming (and even the command line for that matter!) Thanks! 
#!usr/bin/perl

use strict;
use warnings;

my $infile = "xxx_capillary_SNPs.txt\n"; #I'm identifying the file I w
+ant to open

open $infile = <STDIN> || die "open infile failed\n"; #opening the inp
+ut file
chomp ($infile); #I'm trying to keep the first column and header rows 
+of the file I'm opening for use in the output file

my $A = 'T'; #change A to T
my $C = 'G'; #change C to G
my $G = 'G'; #change G to C
my $T = 'A'; #change T to A
{
open $outfile = "$file + _revcomp\n" || die "open outfile failed\n"; #
+I want to make a new file entitled "xxx_capillary_SNPs_revcomp.txt as
+ the outputfile
    print $A, $C, $G, $T to 
}
    print $outfile "\n";
    close $infile

close $outfile;

print "script complete\n";

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In reply to Another Reverse Complement Question... by lkenefic

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