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1 #! /usr/bin/perl
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2
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3 my($input, $SIZE) = @ARGV;
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4 open(IN, "<$input") or die "Can't open $input for reading!\n";
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5
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6 #chr1 genetrack . 123950 123970 22 + . stddev=0.0
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7 #chr1 genetrack . 565745 565765 12 + . stddev=0.0
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8 #chr1 genetrack . 565793 565813 44 + . stddev=0.298065387468
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9
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10 $line = "";
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11 while($line = <IN>) {
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12 chomp($line);
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13 @array = split(/\t/, $line);
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14
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15 $CENTER = int(($array[3] + $array[4]) / 2);
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16 if(($array[4] - $array[3]) % 2 != 0 || $array[6] eq "-") { $CENTER++; }
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17 $START = $CENTER - ($SIZE / 2);
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18 $STOP = $CENTER + (($SIZE / 2) - 1);
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19
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20 if($START < 1) { print STDERR "Error:\t$line\nRequested expansion places region beyond chromosome bounds!!!\n"; }
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21 else {
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22 print "$array[0]\t$array[1]\t$array[2]\t$START\t$STOP";
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23 for($x = 5; $x <= $#array; $x++) { print "\t$array[$x]"; }
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24 print "\n";
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25 }
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26 }
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27 close IN;
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