用perl计算序列中各种核苷酸频数并将其导入文件

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 = ;

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 = ;

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;