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1 #!/usr/bin/env perl
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2
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3 use strict;
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4 use warnings;
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5
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6 #this merges the significance output with the SNPs so users get more than an index
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7
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8 my($out, $snp) = @ARGV;
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9
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10 if (!$out or !$snp) { die "missing args\n"; }
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11
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12 #merge SNP data with results
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13 merge();
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14
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15 exit;
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16
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17 ########################################
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18
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19 #merge the input and output files so have SNP data with result
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20 sub merge {
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21 open(FH, $out) or die "Couldn't open $out, $!\n";
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22 my %res;
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23 my @ind;
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24 while (<FH>) {
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25 chomp;
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26 my $line = $_;
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27 #0: 10 score= 14.224153 , df= 2 , p= 0.040760 , N=50
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28 if ($line =~ /^(\d+):\s+(.*)/) { $res{$1} = $2; push(@ind, $1); }
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29 }
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30 close FH;
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31 if (!@ind) { return; } #no results, leave alone
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32 @ind = sort { $a <=> $b } @ind;
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33 #read input file to get SNP data
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34 open(FH, $snp) or die "Couldn't open $snp, $!\n";
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35 my $i = 0; #0 based, not counting ID line
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36 my $c = shift @ind;
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37 while (<FH>) {
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38 chomp;
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39 if (/^ID/) { next; }
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40 my @f = split(/\s+/);
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41 if ($i == $c) {
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42 $res{$i} = "$f[0]\t$f[1]\t$f[2]\t$res{$i}";
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43 if (!@ind) { last; }
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44 $c = shift @ind;
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45 }
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46 $i++;
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47 }
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48 close FH;
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49 #now reprint results with SNP data included
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50 open(FH, ">", $out) or die "Couldn't write to $out, $!\n";
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51 print FH "ID\tchr\tposition\tresults\n";
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52 foreach $i (keys %res) {
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53 print FH $res{$i}, "\n";
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54 }
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55 close FH;
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56 }
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57
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