1:http://www.jianshu.com/p/824a94f92007
2:http://www.jianshu.com/p/dd6f4192abe5
#!/usr/bin/perl -w
# Determining frequency of nucleotides, take 3
# Get the DNA sequence data
print "Please type the filename of the DNA sequence data: ";
$dna_filename = <STDIN>;
chomp $dna_filename;
# Does the file exist?
unless ( -e $dna_filename) {
print "File \"$dna_filename\" doesn\'t seem to exist!!\n";
exit;
}
# Can we open the file?
unless ( open(DNAFILE, $dna_filename) ) {
print "Cannot open file \"$dna_filename\"\n\n";
exit;
}
@DNA = <DNAFILE>;
close DNAFILE;
$DNA = join( '', @DNA);
# Remove whitespace
$DNA =~ s/\s//g;
# Initialize the counts.
# Notice that we can use scalar variables to hold numbers.
$a = 0; $c = 0; $g = 0; $t = 0; $e = 0;
# Use a regular expression "trick", and five while loops,
# to find the counts of the four bases plus errors
while($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";
# Also write the results to a file called "countbase"
$outputfile = "countbase";
unless ( open(COUNTBASE, ">$outputfile") ) {
print "Cannot open file \"$outputfile\" to write to!!\n\n";
exit;
}
print COUNTBASE "A=$a C=$c G=$g T=$t errors=$e\n";
close(COUNTBASE);
# exit the program
exit;
