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Perl script to Mutate a DNA Sequence

  • Public
By Anjana 529 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); }