Name	Chr	Position
rs1	1	35251
rs2	1	35248
rs3	1	37514
rs4	1	21145
rs5	2	35150
rs6	3	11412
rs7	4	7721
rs8	21	42516
rs9	4	1110
rs10	4	1145

##</code><code>##

PGX_SOLEXA1:2:1:5:804#0/1	-	chr1	35245	GGGAGGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAA	BB^Yaa^a\a\D\aaaaa`V`a``abbaabaabaaa	0	"24:A>N,34:T>N"
PGX_SOLEXA1:2:4:5:804#0/1	+	chr1	37510	TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	BB^Yaa^a\a\D\aaaaa`V`a``abbaabaabaaa	0	"24:A>N,34:T>N"
PGX_SOLEXA1:4:4:5:804#0/1	-	chr1	21140	CCCCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	BB^Yaa^a\a\D\aaaaa`V`a``abbaabaabaaa	0	"24:A>N,34:T>N"
PGX_SOLEXA1:4:4:5:774#0/1	-	chr2	35128	AAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAA	BB^Yaa^a\a\D\aaaaa`V`a``abbaabaabaaa	0	"24:A>N,34:T>N"
PGX_SOLEXA1:4:8:5:474#0/1	+	chr3	11410	CCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	BB^Yaa^a\a\D\aaaaa`V`a``abbaabaabaaa	21	"24:A>N,34:T>N"
PGX_SOLEXA1:4:8:5:314#0/1	+	chr5	7720	AGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA	BB^Yaa^a\a\D\aaaaa`V`a``abbaabaabaaa	0	"24:A>N,34:T>N"
PGX_SOLEXA1:15:8:5:314#0/1	-	chr21	42510	GGGGGGTCCCCCCCCCCCCCCCCCCCCCCCCCCCCC	BB^Yaa^a\a\D\aaaaa`V`a``abbaabaabaaa	0	"24:A>N,34:T>N"
PGX_SOLEXA1:4:9:5:314#0/1	-	chr1	35239	AAAAAAGGGAGGTAAAAAAAAAAAAAAAAAAAAAAA	BB^Yaa^a\a\D\aaaaa`V`a``abbaabaabaaa	0	"24:A>N,34:T>N"
PGX_SOLEXA1:4:9:21:314#0/1	+	chr4	1110	GAAAAAGGGAGGTAAAAAAAAAAAAAAAAAAAAAAG	BB^Yaa^a\a\D\aaaaa`V`a``abbaabaabaaa	0	"24:A>N,34:T>N"

##</code><code>##

!/usr/bin/perl

# filename: Read_Bow_SNP.pl                                             
## Script description: This program takes input and match the chromosome location from Bowtie parser file,
#                     then adds the read # to the window (also including neighboring windows)


## Perl interpreter command
# use warnings;
use strict;
use warnings;

## Hashes initialized
my %input;
my %bowtieP;

my $location = 0;

## Open files


# file1 - input: create window # from position
open (FILE1, "Mock3_SNP.txt");
my $head = <FILE1>; # If there is a header in the input #1, include this code
while (<FILE1>) {
    chomp;
    my $input_orig = $_;
    my @line = split /\s+/, $_;
	my $name = $line[0];
    my $chr = "chr$line[1]";
    my $pos = $line[2];
    $input{$name}[0] = $name;
	$input{$name}[1] = $chr;
	$input{$name}[2] = $pos;
}
close FILE1;

open (OUT, "> test.txt"); ### Change if file name changes
print OUT "ID\tInput chr\tInput pos\tBow ID\tBow strand\tBow chr\tBow pos\tBow pos+35\tSeq\tSNP\n";

open (FILE2, "Mock3_forSNP.bow"); #bow file
while (<FILE2>) {
    chomp;
    my @line = split /\s+/, $_;
	if ($line[6]==0) {
	my $ID = $line[0];
	my $strand = $line[1];
    my $chr = $line[2];
    my $pos = $line[3];
	my $seq = $line[4];
		
	foreach my $name(keys %input) {
		if ($input{$name}[1] eq $chr) {
			if ($input{$name}[2] > $pos-1 && $input{$name}[2] < $pos+36) {
				#print OUT "$input{$name}[0]\t$input{$name}[1]\t$input{$name}[2]\t$ID\t$strand\t$chr\t$pos\t$pos+35\t$seq\n";
				print OUT "$input{$name}[0]\t$input{$name}[1]\t$input{$name}[2]\t$ID\t$strand\t$chr\t$pos\t($pos+35)\t$seq\t";
				if ($input{$name}[2] == $pos) {
					my $fSNP = substr($seq, 0, 1);
					print OUT "$fSNP\n";	
				}
				if ($input{$name}[2] == $pos+35) {
					my $fSNP = substr($seq, 35,1);
					print OUT "$fSNP\n";	
				}
				if ($input{$name}[2] != $pos+35 && $input{$name}[2] != $pos) {
					my $SNP = substr($seq, 0, $input{$name}[2]-($pos-1));
					my $fSNP = substr($SNP, $input{$name}[2]-$pos);		
					print OUT "$fSNP\n";	
				}	
				}
			}		
		}
	}	
}
close FILE2;
close OUT;