Mercurial > repos > greg > resize_coordinate_window

comparison resize_coordinate_window.pl @ 0:d64206d13298 draft default tip

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author greg
date Wed, 06 Jan 2016 15:15:56 -0500
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-1:000000000000 0:d64206d13298
1 #! /usr/bin/perl
2
3 my($input, $SIZE) = @ARGV;
4 open(IN, "<$input") or die "Can't open $input for reading!\n";
5
6 #chr1 genetrack . 123950 123970 22 + . stddev=0.0
7 #chr1 genetrack . 565745 565765 12 + . stddev=0.0
8 #chr1 genetrack . 565793 565813 44 + . stddev=0.298065387468
9
10 $line = "";
11 while($line = <IN>) {
12 chomp($line);
13 @array = split(/\t/, $line);
14
15 $CENTER = int(($array[3] + $array[4]) / 2);
16 if(($array[4] - $array[3]) % 2 != 0 || $array[6] eq "-") { $CENTER++; }
17 $START = $CENTER - ($SIZE / 2);
18 $STOP = $CENTER + (($SIZE / 2) - 1);
19
20 if($START < 1) { print STDERR "Error:\t$line\nRequested expansion places region beyond chromosome bounds!!!\n"; }
21 else {
22 print "$array[0]\t$array[1]\t$array[2]\t$START\t$STOP";
23 for($x = 5; $x <= $#array; $x++) { print "\t$array[$x]"; }
24 print "\n";
25 }
26 }
27 close IN;