Differences

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--- gc_skew.pl [2016/02/18 09:15] – created hyjeong
+++ gc_skew.pl [2021/03/17 13:09] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-!/usr/bin/perl
+  #!/usr/bin/perl
-use Bio::SeqIO;
+  use Bio::SeqIO;
-$window = 5000; # 10 kb
+  $window = 5000; # 10 kb
-$shift = 5000;   # 2 kb
+  $shift = 5000;   # 2 kb
-$seqIn = Bio::SeqIO->new(-file => $ARGV[0], -format => 'fasta');
+  $seqIn = Bio::SeqIO->new(-file => $ARGV[0], -format => 'fasta');
-$seqObj = $seqIn->next_seq();
+  $seqObj = $seqIn->next_seq();
-$seqStr = $seqObj->seq();
+  $seqStr = $seqObj->seq();
-$length = $seqObj->length();
+  $length = $seqObj->length();
-@whole_seq = split //, $seqStr;
+  @whole_seq = split //, $seqStr;
-$cum_GC_skew = 0;
+  $cum_GC_skew = 0;
-for ($i = 1; $i <= $length; $i += $shift) {
+  for ($i = 1; $i <= $length; $i += $shift) {
-    $end = $i + $shift - 1;
+      $end = $i + $shift - 1;
-    $end = $length if $end > $length;
+      $end = $length if $end > $length;
-    $frag = $seqObj->trunc($i, $end)->seq();
+      $frag = $seqObj->trunc($i, $end)->seq();
-    $G = ($frag =~ s/g/G/ig);
+      $G = ($frag =~ s/g/G/ig);
-    $C = ($frag =~ s/c/C/ig);
+      $C = ($frag =~ s/c/C/ig);
-    $GC_skew = ($G - $C) / ($G + $C);
+      $GC_skew = ($G - $C) / ($G + $C);
-    $cum_GC_skew += $GC_skew;
+      $cum_GC_skew += $GC_skew;
-    $GC = ($G + $C) / $window;
+      $GC = ($G + $C) / $window;
-    print join "\t", $i, $GC_skew, $cum_GC_skew, $GC . "\n";
+      print join "\t", $i, $GC_skew, $cum_GC_skew, $GC . "\n";
+  }
-}