Counting Nucleotides
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#!/usr/bin/perl -w
print "Please type filename of DNA sequence data: ";
$dna_filename = <STDIN>;
chomp $dna_filename;
unless ( -e dna_filename ) {
print "FILE NOT FOUND\n";
exit;
} unless( open(DNAFILE, $dna_filename) ){
print "CANNOT OPEN FILE\n";
exit;
}
@DNA = <DNAFILE>;
close DNAFILE;
$DNA = join('',@DNA);
$DNA =~ s/\s//g;
#remove whitespace
$a=0;
$c=0;
$g=0;
$t=0;
$e=0;
while($DNA =~ /a/ig) {$a++}
while($DNA =~ /c/ig) {$c++}
while($DNA =~ /g/ig) {$g++}
while($DNA =~ /t/ig) {$t++}
while($DNA =~ /[^acgt]/ig) {$e++}
print "A=$a, C=$c, G=$g, T=$t, errors=$e\n";
$outputfile = "countbase";
unless ( open(COUNTBASE, ">$outputfile") ) {
print "CANNOT OPEN FILE\n";
exit;
}
print COUNTBASE "A=$a, C=$c, G=$g, T=$t, errors=$e\n";
close(COUNTBASE);
exit;
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