Rahul Nayak
A Bioinformatician
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Calculate Dinucleotide Frequency with Perl
By Rahul Nayak 2539 days ago
#!/usr/bin/perl -w
use strict;
my ($genome, $head, $tail);
my (%mono_nt, %di_nt);
$/ = ">";
open my $fasta, '<', $ARGV[0] or die $!;
while (<$fasta>) {
chomp; s/\r//g; s/^\s*|\s*$//;
if (/.+?\n(.+)/s) {
(my $seq = $1) =~ s/\n//g;
$genome .= uc $seq;
$head = uc substr($seq, 0, 1);
$di_nt{"$tail$head"}-- if $tail;
$tail = uc substr($seq, -1);
}
}
close $fasta;
my $len = length $genome;
for my $i (0..$len-2) {
my $each_mono_nt = substr($genome, $i, 1);
my $each_di_nt = substr($genome, $i, 2);
$mono_nt{$each_mono_nt}++;
$di_nt{$each_di_nt}++;
}
$mono_nt{$tail}++;
print "-"x30, "\nSingle nucleotide frequency:\n";
for my $nt (sort keys %mono_nt) {print "$nt\t", $mono_nt{$nt} / $len, "\n";}
print "\n", "-"x30, "\nDinucleotide frequency:\nDinucleotide\tObs. freq.\tExp. freq.\n";
for my $nt_pair (sort keys %di_nt) {
my ($first_nt, $second_nt) = split //, $nt_pair;
print "$nt_pair\t", $di_nt{$nt_pair} / ($len-1), "\t",
$mono_nt{$first_nt} * $mono_nt{$second_nt} /$len /$len, "\n";
}
