#!/usr/bin/perl
use strict;
use Data::Dumper;
use Storable;


## 5_prime_ref.fasta => 
# >chr1   67093601        67093610        CTACAGGAA
# >chr1   67095418        67095427        TTTCAGAAA
# >chr1   67096318        67096327        TTTCAGCTC
# >chr1   67115461        67115470        TTCCAGGCA
# >chr1   67125906        67125915        CTGCAGATA
# >chr1   67127254        67127263        AAATAGGAA
# >chr1   67131224        67131233        TAATAGATT
# >chr1   67093601        67093610        CTACAGGAA
# >chr1   67096318        67096327        TTTCAGCTC
# >chr1   67103379        67103388        GTTTAGATG
# >chr1   67111641        67111650        CTTTAGAGC
# >chr1   67115461        67115470        TTCCAGGCA
# >chr1   67125906        67125915        CTGCAGATA
# >chr1   67127254        67127263        AAATAGGAA
# >chr1   67131224        67131233        TAATAGATT
# >chr1   67093601        67093610        CTACAGGAA
# >chr1   67096318        67096327        TTTCAGCTC
# >chr1   67103379        67103388        GTTTAGATG
# >chr1   67111641        67111650        CTTTAGAGC
# >chr1   67113753        67113762        ATATAGTGA
# >chr1   201324579       201324588       GGGTAAGGT


open my $fasta5, '<', '5_prime_ref.fasta';
chomp (my @fasta5 = <$fasta5>);
close $fasta5;



my ($altsequence1, $altsequence2, $altsequence3, @newfasta5, @newfasta3, $sequence, @splity, $test, $j, $genomicposition, $ref, $alt1, $alt2, $alt3, $refsequence);
## for 5 prime ## >chr1   201324579       201324588       GGGTAAGGT
foreach my $line (@fasta5) { 
## need to iterate 9 times through j... 
	$j = 0;
	while ($j < 9) {
	@splity = split ("\t", $line);
	my $ref = $splity[3];
	$sequence = $splity[3];
	$refsequence = $splity[3];
	$genomicposition = $splity[1];
	$genomicposition = $genomicposition + 1; #first nucleotide is counted as first column + 1, not as the left boundary
	$splity[0] = ">".$splity[0];
	
	##if ($character $j in sequence =~ matches A) {
	if (substr ($sequence, $j, 1) =~ m/A/) {
	$ref = "A";
	$genomicposition = $genomicposition + $j;
	$test = substr ($sequence, $j, 1);
	$sequence =~ s/$test/C/;
	$altsequence1 = $sequence;
	$alt1 = "C";
	$test = substr ($sequence, $j, 1);
	$sequence =~ s/$test/G/;
	$altsequence2 = $sequence;
	$alt2 = "G";
	$test = substr ($sequence, $j, 1);
	$sequence =~ s/$test/T/;
	$altsequence3 = $sequence;
	$alt3 = "T";
		}

	elsif (substr ($sequence, $j, 1) =~ m/C/) {
	$test = substr ($sequence, $j, 1);
	$ref = "C";
	$genomicposition = $genomicposition + $j;
	$sequence =~ s/$test/A/;
	$altsequence1 = $sequence;
	$alt1 = "A";
	$test = substr ($sequence, $j, 1);
	$sequence =~ s/$test/G/;
	$altsequence2 = $sequence;
	$alt2 = "G";
	$test = substr ($sequence, $j, 1);
	$sequence =~ s/$test/T/;
	$altsequence3 = $sequence;
	$alt3 = "T";
	}
	
	elsif (substr ($sequence, $j, 1) =~ m/T/) {
	$test = substr ($sequence, $j, 1);
	$ref = "T";
	$genomicposition = $genomicposition + $j;
	$sequence =~ s/$test/A/;
	$altsequence1 = $sequence;
	$alt1 = "A";
	$test = substr ($sequence, $j, 1);
	$sequence =~ s/$test/G/;
	$altsequence2 = $sequence;
	$alt2 = "G";
	$test = substr ($sequence, $j, 1);
	$sequence =~ s/$test/C/;
	$altsequence3 = $sequence;
	$alt3 = "C";
	}
			
	else {  	
	$ref = "G";
	$genomicposition = $genomicposition + $j;
	$test = substr ($sequence, $j, 1);
	$sequence =~ s/$test/A/;
	$altsequence1 = $sequence;
	$alt1 = "A";
	$test = substr ($sequence, $j, 1);
	$sequence =~ s/$test/T/;
	$altsequence2 = $sequence;
	$alt2 = "T";
	$test = substr ($sequence, $j, 1);
	$sequence =~ s/$test/C/;
	$altsequence3 = $sequence;
	$alt3 = "C";
			}
			
	
	## print the new 3 lines		
	my $newfasta5alt1 = join ("\t", $refsequence, $splity[0], $splity[1], $splity[2], $altsequence1, $ref, $alt1, $genomicposition);
	my $newfasta5alt2 = join ("\t", $refsequence, $splity[0], $splity[1], $splity[2], $altsequence2, $ref, $alt2, $genomicposition);
	my $newfasta5alt3 = join ("\t", $refsequence, $splity[0], $splity[1], $splity[2], $altsequence3, $ref, $alt3, $genomicposition);
	
	my $newfasta5 = join ("\n", $newfasta5alt1, $altsequence1, $newfasta5alt2, $altsequence2, $newfasta5alt3, $altsequence3); 
	push (@newfasta5, $newfasta5);
	$j++;}
next;
	}
	
	print Dumper @newfasta5;