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1 #! /usr/bin/perl -w
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2
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3 use strict;
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4 use warnings;
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5 use File::Temp "tempfile";
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6
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7 my ($input1, $input2, $field1, $field2, $mode, $OOption, $out_file1) = @ARGV;
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8
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9 die "No arguments\n" unless @ARGV == 7;
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10
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11 my ($fh1, $file1) = tempfile();
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12 my ($fh2, $file2) = tempfile();
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13
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14 `sort -k $field1 $input1 > $file1`;
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15 `sort -k $field2 $input2 > $file2`;
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16
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17 my $option = "";
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18 my @fields = ();
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19 my $line = "";
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20
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21 if ($OOption eq "Y") {
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22 if (defined($fh1)) {
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23 $line = <$fh1>;
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24 } else {
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25 die "Failed to create file $file1\n";
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26 }
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27 @fields = split /\t/, $line;
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28 die "The field you selected does not exist in the input file" if (@fields < $field1);
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29 my @optionO = ();
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30 my $i = 0;
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31 foreach (@fields) {
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32 ++$i;
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33 push(@optionO, "1.$i");
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34 }
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35 $option = "-o " . join(",", @optionO);
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36 } else {
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37 $option = "";
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38 }
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39
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40 $ENV{'LC_ALL'} = 'POSIX';
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41
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42 if ($mode eq "V") {
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43 `join -v 1 $option -1 $field1 -2 $field2 $file1 $file2 | tr " " "\t" > $out_file1`;
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44 } else {
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45 `join $option -1 $field1 -2 $field2 $file1 $file2 | tr " " "\t" > $out_file1`;
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46 }
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47
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48 `rm $file1 ; rm $file2`;
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49
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50
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51
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