Perl script to Mutate a DNA Sequence
By Anjana 2897 days ago
#!/usr/local/bin/perl -w
# This script randomly mutates the DNA sequence and generates 10 successive mutation results.
# While executing this script it asks for the file name of the DNA sequence.
# If the DNA sequence file is not in the same directory of this script, enter the file name with its full path.
# Example:
# In windows: c:\rnafile.txt
# In Linux : /home/user/sequence/rnafile.txt
use File::Path;
print "ENTER THE FILENAME OF THE DNA SEQUENCE:= ";
$dnafilename = <STDIN>;
chomp $dnafilename;
unless ( open(DNAFILE, $dnafilename) )
{
print "Cannot open file \"$dnafilename\"\n\n";
goto h;
}
my $DNA = <DNAFILE>;
close DNAFILE;
my $i;
my $mutant;
$mutant = mutate($DNA);
print "Mutate DNA\n\n";
print "HERE ARE THE 10 SUCCESSIVE MUTATIONS:\n\n";
for ($i=0 ; $i < 10 ; ++$i)
{
$mutant = mutate($mutant);
print "$mutant\n";
print WRITE "$mutant\n";
}
sub mutate
{
my($dna) = @_;
my($position) = randomposition($dna);
my $current_base = substr($dna, $position, 1);
my $newbase;
do
{
$newbase = randomnucleotide();
}
until ($newbase ne $current_base);
substr($dna,$position,1,$newbase);
return $dna;
}
sub randomposition
{
my($string) = @_;
return int rand length $string;
}
sub randomelement
{
my(@array) = @_;
return $array[rand @array];
}
sub randomnucleotide
{
my(@nucleotides) = ('A', 'C', 'G', 'T');
return randomelement(@nucleotides);
}
