gc_skew.pl
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!/usr/bin/perl
use Bio::SeqIO;
$window = 5000; # 10 kb $shift = 5000; # 2 kb
$seqIn = Bio::SeqIO→new(-file ⇒ $ARGV[0], -format ⇒ 'fasta'); $seqObj = $seqIn→next_seq(); $seqStr = $seqObj→seq(); $length = $seqObj→length(); @whole_seq = split , $seqStr; $cum_GC_skew = 0; for ($i = 1; $i ⇐ $length; $i += $shift) { $end = $i + $shift - 1; $end = $length if $end > $length; $frag = $seqObj→trunc($i, $end)→seq(); $G = ($frag =~ s/g/G/ig); $C = ($frag =~ s/c/C/ig); $GC_skew = ($G - $C) / ($G + $C); $cum_GC_skew += $GC_skew; $GC = ($G + $C) / $window; print join “\t”, $i, $GC_skew, $cum_GC_skew, $GC . “\n”; }
gc_skew.pl.1455754524.txt.gz · Last modified: (external edit)