Who can program (specifically, in Perl)?

[Magrathean]

I finally finished the little program i'd been working on since last year. It's nothing too great or useful, but i'm proud of it. It's the first thing i really program on my own (i.e. without a book by my side telling me exactly what to do and only letting me change the font size), so don't burst my bubble for a while.

Anywho, here it is (in case anyone cares): a little program which compares two DNA sequences and finds any mutations in them:

print "\n\nWelcome.\n\nWe will compare two DNA sequences and analyze any mutations.\n\nPlease choose a sequence length (in multiples of 3): ";
$length=<STDIN>;
while ($length%3!=0)
	{
		print "That is not a multiple of 3. Please choose another sequence length: ";
		$length=<STDIN>;
	}
print "\nVery well. Now write the first sequence.\n";
$nt=1;
while ($nt<=$length)
	{
		print "Nucleotide $nt: ";
		$seq1[$nt]=<STDIN>;
		if (($seq1[$nt]=~"A")||($seq1[$nt]=~"a"))
			{
				$seq1[$nt]='A';
				$nt++;
			}
		elsif (($seq1[$nt]=~"C")||($seq1[$nt]=~"c"))
			{
				$seq1[$nt]='C';
				$nt++;
			}
		elsif (($seq1[$nt]=~"G")||($seq1[$nt]=~"g"))
			{
				$seq1[$nt]='G';
				$nt++;
			}
		elsif (($seq1[$nt]=~"T")||($seq1[$nt]=~"t"))
			{
				$seq1[$nt]='T';
				$nt++;
			}
		elsif (($seq1[$nt]=~"U")||($seq1[$nt]=~"u"))
			{
				print "Uracil only exists in RNA. We are working with DNA.\n";
			}
		else
			{
				print "That nucleotide doesn't exist. Please write A, C, G or T.\n";
			}
	}
print "\nNow write the second sequence.\n";
$nt=1;
while ($nt<=$length)
	{
		print "Nucleotide $nt: ";
		$seq2[$nt]=<STDIN>;
		if (($seq2[$nt]=~"A")||($seq2[$nt]=~"a"))
			{
				$seq2[$nt]='A';
				$nt++;
			}
		elsif (($seq2[$nt]=~"C")||($seq2[$nt]=~"c"))
			{
				$seq2[$nt]='C';
				$nt++;
			}
		elsif (($seq2[$nt]=~"G")||($seq2[$nt]=~"g"))
			{
				$seq2[$nt]='G';
				$nt++;
			}
		elsif (($seq2[$nt]=~"T")||($seq2[$nt]=~"t"))
			{
				$seq2[$nt]='T';
				$nt++;
			}
		elsif (($seq2[$nt]=~"U")||($seq2[$nt]=~"u"))
			{
				print "Uracil only exists in RNA. We are working with DNA.\n";
			}
		else
			{
				print "That nucleotide doesn't exist. Please write A, C, G or T.\n";
			}
		}
print "\nVerification:\n\nSequence 1: ";
$nt=1;
while ($nt<=$length)
	{
		print ("$seq1[$nt]");
		$nt++;
	}
$nt=1;
print ("\nSequence 2: ");
while ($nt<=$length)
	{
		print ("$seq2[$nt]");
		$nt++;
	}
print "\n\nIs this correct? (y/n) ";
$yes=<STDIN>;
while (($yes!=~"y")&&($yes!=~"Y")&&($yes!=~"n")&&($yes!=~"N"))
	{
		print ("Please state whether these sequences are correct (y/n): ");
		$yes=<STDIN>;
	}
while (($yes=~"n")||($yes=~"N"))
	{
		print "\nWrite the first sequence again.\n";
		$nt=1;
		while ($nt<=$length)
			{
				print "Nucleotide $nt: ";
				$seq1[$nt]=<STDIN>;
				if (($seq1[$nt]=~"A")||($seq1[$nt]=~"a"))
					{
						$seq1[$nt]="A";
						$nt++;
					}
				elsif (($seq1[$nt]=~"C")||($seq1[$nt]=~"c"))
					{
						$seq1[$nt]="C";
						$nt++;
					}
				elsif (($seq1[$nt]=~"G")||($seq1[$nt]=~"g"))
					{
						$seq1[$nt]="G";
						$nt++;
					}
				elsif (($seq1[$nt]=~"T")||($seq1[$nt]=~"t"))
					{
						$seq1[$nt]="T";
						$nt++;
					}
				elsif (($seq1[$nt]=~"U")||($seq1[$nt]=~"u"))
					{
						print "Uracil only exists in RNA. We are working with DNA.\n";
					}
				else
					{
						print "That nucleotide doesn't exist. Please write A, C, G or T.\n";
					}
			}
		print "\nNow write the second sequence.\n";
		$nt=1;
		while ($nt<=$length)
			{
				print "Nucleotide $nt: ";
				$seq2[$nt]=<STDIN>;
				if (($seq2[$nt]=~"A")||($seq2[$nt]=~"a"))
					{
						$seq2[$nt]="A";
						$nt++;
					}
				elsif (($seq2[$nt]=~"C")||($seq2[$nt]=~"c"))
					{
						$seq2[$nt]="C";
						$nt++;
					}
				elsif (($seq2[$nt]=~"G")||($seq2[$nt]=~"g"))
					{
						$seq2[$nt]="G";
						$nt++;
					}
				elsif (($seq2[$nt]=~"T")||($seq2[$nt]=~"t"))
					{
						$seq2[$nt]="T";
						$nt++;
					}
				elsif (($seq2[$nt]=~"U")||($seq2[$nt]=~"u"))
					{
						print "Uracil only exists in RNA. We are working with DNA.\n";
					}
				else
					{
						print "That nucleotide doesn't exist. Please write A, C, G or T.\n";
					}
				}
		print "\nVerification:\n\nSequence 1: ";
		$nt=1;
		while ($nt<=$length)
			{
				print ("$seq1[$nt]");
				$nt++;
			}
		$nt=1;
		print ("\nSequence 2: ");
		while ($nt<=$length)
			{
				print ("$seq2[$nt]");
				$nt++;
			}
		print "\n\nIs this correct? (y/n) ";
		$yes=<STDIN>;
	}
if (($yes=~"y")||($yes=~"Y"))
	{
		print "\nProcessing...\n\n";
		$identical=1;
		$nt=1;
		while ($nt<=$length)
			{
				if ($seq1[$nt] eq $seq2[$nt])
					{
						$mutation[$nt]=0;
					}
				else
					{
						$mutation[$nt]=1;
						$identical=0;
					}
				$nt++;
			}
		$nt=1;
		$aa=1;
		while ($nt<=$length)
			{
				if (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "C"))
					{
						$aa1[$aa]="alanine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] ne "T"))
					{
						$aa1[$aa]="cysteine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] ne "C"))
					{
						$aa1[$aa]="cysteine";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] ne "C"))
					{
						$aa1[$aa]="aspartate";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] ne "T"))
					{
						$aa1[$aa]="aspartate";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] ne "G"))
					{
						$aa1[$aa]="glutamate";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] ne "A"))
					{
						$aa1[$aa]="glutamate";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "T")&&($seq1[$nt+2] ne "C"))
					{
						$aa1[$aa]="phenylalanine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "T")&&($seq1[$nt+2] ne "T"))
					{
						$aa1[$aa]="phenylalanine";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "G"))
					{
						$aa1[$aa]="glycine";
					}
				elsif (($seq1[$nt] eq "C")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] ne "C"))
					{
						$aa1[$aa]="histidine";
					}
				elsif (($seq1[$nt] eq "C")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] ne "T"))
					{
						$aa1[$aa]="histidine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "T")&&($seq1[$nt+2] ne "G"))
					{
						$aa1[$aa]="isoleucine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "A"))
					{
						$aa1[$aa]="lysine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "G"))
					{
						$aa1[$aa]="lysine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "T")&&($seq1[$nt+2] eq "G"))
					{
						$aa1[$aa]="leucine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "T")&&($seq1[$nt+2] eq "A"))
					{
						$aa1[$aa]="leucine";
					}
				elsif (($seq1[$nt] eq "C")&&($seq1[$nt+1] eq "T"))
					{
						$aa1[$aa]="leucine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "T")&&($seq1[$nt+2] eq "G"))
					{
						$aa1[$aa]="methionine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "C"))
					{
						$aa1[$aa]="asparagine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "T"))
					{
						$aa1[$aa]="asparagine";
					}
				elsif (($seq1[$nt] eq "C")&&($seq1[$nt+1] eq "C"))
					{
						$aa1[$aa]="proline";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "G"))
					{
						$aa1[$aa]="glutamine";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "A"))
					{
						$aa1[$aa]="glutamine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] eq "G"))
					{
						$aa1[$aa]="arginine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] eq "A"))
					{
						$aa1[$aa]="arginine";
					}
				elsif (($seq1[$nt] eq "C")&&($seq1[$nt+1] eq "G"))
					{
						$aa1[$aa]="arginine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] eq "T"))
					{
						$aa1[$aa]="serine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] eq "C"))
					{
						$aa1[$aa]="serine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "C"))
					{
						$aa1[$aa]="serine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "C"))
					{
						$aa1[$aa]="threonine";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "T"))
					{
						$aa1[$aa]="valine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] eq "G"))
					{
						$aa1[$aa]="tryptophan";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "T"))
					{
						$aa1[$aa]="tyrosine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "C"))
					{
						$aa1[$aa]="tyrosine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "A"))
					{
						$aa1[$aa]="a stop codon";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] eq "A"))
					{
						$aa1[$aa]="a stop codon";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "G"))
					{
						$aa1[$aa]="a stop codon";
					}
				$nt+=3;
				$aa++;
			}
		$nt=1;
		$aa=1;
		while ($nt<=$length)
			{
				if (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "C"))
					{
						$aa2[$aa]="alanine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] ne "T"))
					{
						$aa2[$aa]="cysteine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] ne "C"))
					{
						$aa2[$aa]="cysteine";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] ne "C"))
					{
						$aa2[$aa]="aspartate";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] ne "T"))
					{
						$aa2[$aa]="aspartate";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] ne "G"))
					{
						$aa2[$aa]="glutamate";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] ne "A"))
					{
						$aa2[$aa]="glutamate";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "T")&&($seq2[$nt+2] ne "C"))
					{
						$aa2[$aa]="phenylalanine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "T")&&($seq2[$nt+2] ne "T"))
					{
						$aa2[$aa]="phenylalanine";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "G"))
					{
						$aa2[$aa]="glycine";
					}
				elsif (($seq2[$nt] eq "C")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] ne "C"))
					{
						$aa2[$aa]="histidine";
					}
				elsif (($seq2[$nt] eq "C")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] ne "T"))
					{
						$aa2[$aa]="histidine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "T")&&($seq2[$nt+2] ne "G"))
					{
						$aa2[$aa]="isoleucine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "A"))
					{
						$aa2[$aa]="lysine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "G"))
					{
						$aa2[$aa]="lysine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "T")&&($seq2[$nt+2] eq "G"))
					{
						$aa2[$aa]="leucine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "T")&&($seq2[$nt+2] eq "A"))
					{
						$aa2[$aa]="leucine";
					}
				elsif (($seq2[$nt] eq "C")&&($seq2[$nt+1] eq "T"))
					{
						$aa2[$aa]="leucine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "T")&&($seq2[$nt+2] eq "G"))
					{
						$aa2[$aa]="methionine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "C"))
					{
						$aa2[$aa]="asparagine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "T"))
					{
						$aa2[$aa]="asparagine";
					}
				elsif (($seq2[$nt] eq "C")&&($seq2[$nt+1] eq "C"))
					{
						$aa2[$aa]="proline";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "G"))
					{
						$aa2[$aa]="glutamine";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "A"))
					{
						$aa2[$aa]="glutamine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] eq "G"))
					{
						$aa2[$aa]="arginine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] eq "A"))
					{
						$aa2[$aa]="arginine";
					}
				elsif (($seq2[$nt] eq "C")&&($seq2[$nt+1] eq "G"))
					{
						$aa2[$aa]="arginine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] eq "T"))
					{
						$aa2[$aa]="serine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] eq "C"))
					{
						$aa2[$aa]="serine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "C"))
					{
						$aa2[$aa]="serine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "C"))
					{
						$aa2[$aa]="threonine";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "T"))
					{
						$aa2[$aa]="valine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] eq "G"))
					{
						$aa2[$aa]="tryptophan";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "T"))
					{
						$aa2[$aa]="tyrosine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "C"))
					{
						$aa2[$aa]="tyrosine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "A"))
					{
						$aa2[$aa]="a stop codon";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] eq "A"))
					{
						$aa2[$aa]="a stop codon";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "G"))
					{
						$aa2[$aa]="a stop codon";
					}
				$nt+=3;
				$aa++;
			}
		$nt=1;
		$aa=1;
		if ($identical==1)
			{
				print "The two sequences are identical.\n\n";
			}
		else
			{
				$mutationcounter=0;
				while ($nt<=$length)
					{
						$mutationcounter=0;
						if ($mutation[$nt]==1)
							{
								$mutationcounter++;
								$aa=($nt+2)/3;
							}
						if ($mutation[$nt+1]==1)
							{
								$mutationcounter++;
								$aa=($nt+2)/3;
							}
						if ($mutation[$nt+2]==1)
							{
								$mutationcounter++;
								$aa=($nt+2)/3;
							}
						if ($mutationcounter==1)
							{
								print "There is one ";
								if ($aa1[$aa] eq $aa2[$aa])
									{
										print "synonymous mutation in codon $aa.\n";
									}
								else
									{
										print "mutation in codon $aa which causes $aa2[$aa] to substitute $aa1[$aa].\n";
									}
							}
						elsif ($mutationcounter==2)
							{
								print "There are two ";
								if ($aa1[$aa] eq $aa2[$aa])
									{
										print "synonymous mutations in codon $aa.\n";
									}
								else
									{
										print "mutations in codon $aa which cause $aa2[$aa] to substitute $aa1[$aa].\n";
									}
							}
						elsif ($mutationcounter==3)
							{
								print "There are three mutations in codon $aa which cause $aa2[$aa] to substitute $aa1[$aa].\n";
							}
						$nt+=3;
					}
				print "\n";
			}
	}

Questions / comments / suggestions / corrections / dinner invitations?

 

[La Rocque]

There is already a thread for this sort of thing:

http://www.ultimatemetal.com/forum/showthread.php?t=141399

spam on , Al

 

[rahvin]

i say this stays, the other thread was never very successful, this is a specific question to boot, and i don't really see people starting dozens of new ones about computer programming. it's not as if we're on the internet or something.

 

[marduk1507]

Undo, respect! For me its extraterrestrialish.

 

[plintus]

I don't dig Perl, but seems like too many elseif's

 

[Magrathean]

rahvin: Thanks (i think).

mardy: It's not that hard once you learn to read it (almost everything makes sense, and whatever doesn't you just memorize ).

plintus: Those are to tell the program which codons code for which aminoacids.

 

[BastardSonOfGod]

I used to program in C++

 

[Magrathean]

And then what happened?

 

[BastardSonOfGod]

I was in the university studying "Engeneering" but I "froze" my studies to came to sweden to study music... and here I'm

Edited

 

[Magrathean]

Engineering, froze, studies.
[/spellingwhore]

I see. Too bad; programming is cool (well, i like it).

 

[BastardSonOfGod]

Hey thanks for the correction... and yeah, It's very cool, I made like thousand games hahaha, chess and stuffs like that... but finally the music wins and my family support me, because I was interested in music since I was a child, and my parents knew that . It was a very difficult desicion.

 

[Magrathean]

Cool! Finally a couple which supports an art career for their offspring!

So what do you think of my little program?

 

[plintus]

Writing music in C++ is teh best thing eva!!!1!!

 

[BastardSonOfGod]

I didn't test it, well, I never used the Perl language so I don't recognize the librarys but looks familiar, like C++ hahahaha. Questions: why not Java?
This is your first program? a "DNA mutation's finder" is quite original! I made one to find the mass of a star! hahaha oh the good old times...

one more thing... What are you studing? is something related with this or not... maybe you are a self-teached talent

 

[Magrathean]

Perl (...) looks familiar, like C++

It's rather similar. A few changes here and there, and it's easier to use, but i like C++ better.

why not Java?

Because i don't know Java.

This is your first program?

I made a word processor some time ago, but that was kind of copying codes from a book and changing font color, window layout, menu item names and so on, so it doesn't really count. So yes, this is my first program.

a "DNA mutation's finder" is quite original! I made one to find the mass of a star! hahaha oh the good old times...

Thanks! What happened to your star one? I love astronomy.

What are you studing? is something related with this or not...

Genomics (genetics with computers).

maybe you are a self-teached talent

I took basic programming last semester, but some of the codes on that program i made were self-taught (well, with tutorials, but no teachers). And lately i'm trying to teach myself more so i can build upon that program and improve it.

 

[BastardSonOfGod]

My teacher of Algebra was an astronomy lover... he used to measure the mass of the stars for the NASA as a hobbie... so I made the program as a gift... I never used exept when I test it with my teacher of Informatic elements (I don't know the name in English for that signature so that's the literal traduction)... He was very happy ... and about my programs, I left all that in Chile when I came here... so I lost them I think, because My brother bought a new computer for christmas and sold the old one

Anyway good job with the program, Genomics sounds really interesting... and damn difficult too

 

[Magrathean]

I liked your story. It sucks that you've lost those programs, but i suppose you could always program new things as a hobby. And, well, genomics isn't all that difficult (for me, anyway), but it's sure as hell interesting.

 

[Magrathean]

Version 0.2 (new and improved):

print "\n\nWelcome.\n\nWe will compare two DNA sequences and analyze any mutations.\n\nPlease choose a sequence length (in multiples of 3): ";
$length=<STDIN>;
while ($length==0)
	{
		print "Your sequence must have at least three nucleotides. Please choose a sequence length: ";
		$length=<STDIN>;
	}
$res=1;
if ($length%3==0)
	{
		$res=0;
	}
while ($res!=0)
	{
		print "That is not a multiple of 3. Please choose another sequence length: ";
		$length=<STDIN>;
		if ($length%3==0)
			{
				$res=0;
			}
	}
print "\nVery well. Now write the first sequence.\n";
$nt=1;
while ($nt<=$length)
	{
		print "Nucleotide $nt: ";
		$seq1[$nt]=<STDIN>;
		if (($seq1[$nt] eq "A\n")||($seq1[$nt] eq "a\n"))
			{
				$seq1[$nt]='A';
				$nt++;
			}
		elsif (($seq1[$nt] eq "C\n")||($seq1[$nt] eq "c\n"))
			{
				$seq1[$nt]='C';
				$nt++;
			}
		elsif (($seq1[$nt] eq "G\n")||($seq1[$nt] eq "g\n"))
			{
				$seq1[$nt]='G';
				$nt++;
			}
		elsif (($seq1[$nt] eq "T\n")||($seq1[$nt] eq "t\n"))
			{
				$seq1[$nt]='T';
				$nt++;
			}
		elsif (($seq1[$nt] eq "U\n")||($seq1[$nt] eq "u\n"))
			{
				print "Uracil only exists in RNA. We are working with DNA.\n";
			}
		else
			{
				print "That nucleotide doesn't exist. Please write A, C, G or T.\n";
			}
	}
print "\nNow write the second sequence.\n";
$nt=1;
while ($nt<=$length)
	{
		print "Nucleotide $nt: ";
		$seq2[$nt]=<STDIN>;
		if (($seq2[$nt] eq "A\n")||($seq2[$nt] eq "a\n"))
			{
				$seq2[$nt]='A';
				$nt++;
			}
		elsif (($seq2[$nt] eq "C\n")||($seq2[$nt] eq "c\n"))
			{
				$seq2[$nt]='C';
				$nt++;
			}
		elsif (($seq2[$nt] eq "G\n")||($seq2[$nt] eq "g\n"))
			{
				$seq2[$nt]='G';
				$nt++;
			}
		elsif (($seq2[$nt] eq "T\n")||($seq2[$nt] eq "t\n"))
			{
				$seq2[$nt]='T';
				$nt++;
			}
		elsif (($seq2[$nt] eq "U\n")||($seq2[$nt] eq "u\n"))
			{
				print "Uracil only exists in RNA. We are working with DNA.\n";
			}
		else
			{
				print "That nucleotide doesn't exist. Please write A, C, G or T.\n";
			}
		}
print "\nVerification:\nSequence 1: ";
$nt=1;
while ($nt<=$length)
	{
		print "$seq1[$nt]";
		$nt++;
	}
$nt=1;
print "\nSequence 2: ";
while ($nt<=$length)
	{
		print "$seq2[$nt]";
		$nt++;
	}
print "\nIs this correct? (y/n) ";
$yes=<STDIN>;
while (($yes ne "y\n")&&($yes ne "Y\n")&&($yes ne "n\n")&&($yes ne "N\n"))
	{
		print "Please state whether these sequences are correct (y/n): ";
		$yes=<STDIN>;
	}
while (($yes eq "n\n")||($yes eq "N\n"))
	{
		print "\nWrite the first sequence again.\n";
		$nt=1;
		while ($nt<=$length)
			{
				print "Nucleotide $nt: ";
				$seq1[$nt]=<STDIN>;
				if (($seq1[$nt] eq "A\n")||($seq1[$nt] eq "a\n"))
					{
						$seq1[$nt]='A';
						$nt++;
					}
				elsif (($seq1[$nt] eq "C\n")||($seq1[$nt] eq "c\n"))
					{
						$seq1[$nt]='C';
						$nt++;
					}
				elsif (($seq1[$nt] eq "G\n")||($seq1[$nt] eq "g\n"))
					{
						$seq1[$nt]='G';
						$nt++;
					}
				elsif (($seq1[$nt] eq "T\n")||($seq1[$nt] eq "t\n"))
					{
						$seq1[$nt]='T';
						$nt++;
					}
				elsif (($seq1[$nt] eq "U\n")||($seq1[$nt] eq "u\n"))
					{
						print "Uracil only exists in RNA. We are working with DNA.\n";
					}
				else
					{
						print "That nucleotide doesn't exist. Please write A, C, G or T.\n";
					}
			}
		print "\nNow write the second sequence.\n";
		$nt=1;
		while ($nt<=$length)
			{
				print "Nucleotide $nt: ";
				$seq2[$nt]=<STDIN>;
				if (($seq2[$nt] eq "A\n")||($seq2[$nt] eq "a\n"))
					{
						$seq2[$nt]='A';
						$nt++;
					}
				elsif (($seq2[$nt] eq "C\n")||($seq2[$nt] eq "c\n"))
					{
						$seq2[$nt]='C';
						$nt++;
					}
				elsif (($seq2[$nt] eq "G\n")||($seq2[$nt] eq "g\n"))
					{
						$seq2[$nt]='G';
						$nt++;
					}
				elsif (($seq2[$nt] eq "T\n")||($seq2[$nt] eq "t\n"))
					{
						$seq2[$nt]='T';
						$nt++;
					}
				elsif (($seq2[$nt] eq "U\n")||($seq2[$nt] eq "u\n"))
					{
						print "Uracil only exists in RNA. We are working with DNA.\n";
					}
				else
					{
						print "That nucleotide doesn't exist. Please write A, C, G or T.\n";
					}
				}
		print "\nVerification:\nSequence 1: ";
		$nt=1;
		while ($nt<=$length)
			{
				print "$seq1[$nt]";
				$nt++;
			}
		$nt=1;
		print "\nSequence 2: ";
		while ($nt<=$length)
			{
				print "$seq2[$nt]";
				$nt++;
			}
		print "\nIs this correct? (y/n) ";
		$yes=<STDIN>;
	}
if (($yes eq "y\n")||($yes eq "Y\n"))
	{
		print "\nProcessing...\n\n";
		$identical=1;
		$nt=1;
		while ($nt<=$length)
			{
				if ($seq1[$nt] eq $seq2[$nt])
					{
						$mutation[$nt]=0;
					}
				else
					{
						$mutation[$nt]=1;
						$identical=0;
					}
				$nt++;
			}
		$nt=1;
		$aa=1;
		while ($nt<=$length)
			{
				if (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "C"))
					{
						$aa1[$aa]="alanine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] ne "T"))
					{
						$aa1[$aa]="cysteine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] ne "C"))
					{
						$aa1[$aa]="cysteine";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] ne "C"))
					{
						$aa1[$aa]="aspartate";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] ne "T"))
					{
						$aa1[$aa]="aspartate";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] ne "G"))
					{
						$aa1[$aa]="glutamate";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] ne "A"))
					{
						$aa1[$aa]="glutamate";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "T")&&($seq1[$nt+2] ne "C"))
					{
						$aa1[$aa]="phenylalanine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "T")&&($seq1[$nt+2] ne "T"))
					{
						$aa1[$aa]="phenylalanine";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "G"))
					{
						$aa1[$aa]="glycine";
					}
				elsif (($seq1[$nt] eq "C")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] ne "C"))
					{
						$aa1[$aa]="histidine";
					}
				elsif (($seq1[$nt] eq "C")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] ne "T"))
					{
						$aa1[$aa]="histidine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "T")&&($seq1[$nt+2] ne "G"))
					{
						$aa1[$aa]="isoleucine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "A"))
					{
						$aa1[$aa]="lysine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "G"))
					{
						$aa1[$aa]="lysine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "T")&&($seq1[$nt+2] eq "G"))
					{
						$aa1[$aa]="leucine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "T")&&($seq1[$nt+2] eq "A"))
					{
						$aa1[$aa]="leucine";
					}
				elsif (($seq1[$nt] eq "C")&&($seq1[$nt+1] eq "T"))
					{
						$aa1[$aa]="leucine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "T")&&($seq1[$nt+2] eq "G"))
					{
						$aa1[$aa]="methionine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "C"))
					{
						$aa1[$aa]="asparagine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "T"))
					{
						$aa1[$aa]="asparagine";
					}
				elsif (($seq1[$nt] eq "C")&&($seq1[$nt+1] eq "C"))
					{
						$aa1[$aa]="proline";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "G"))
					{
						$aa1[$aa]="glutamine";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "A"))
					{
						$aa1[$aa]="glutamine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] eq "G"))
					{
						$aa1[$aa]="arginine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] eq "A"))
					{
						$aa1[$aa]="arginine";
					}
				elsif (($seq1[$nt] eq "C")&&($seq1[$nt+1] eq "G"))
					{
						$aa1[$aa]="arginine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] eq "T"))
					{
						$aa1[$aa]="serine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] eq "C"))
					{
						$aa1[$aa]="serine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "C"))
					{
						$aa1[$aa]="serine";
					}
				elsif (($seq1[$nt] eq "A")&&($seq1[$nt+1] eq "C"))
					{
						$aa1[$aa]="threonine";
					}
				elsif (($seq1[$nt] eq "G")&&($seq1[$nt+1] eq "T"))
					{
						$aa1[$aa]="valine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] eq "G"))
					{
						$aa1[$aa]="tryptophan";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "T"))
					{
						$aa1[$aa]="tyrosine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "C"))
					{
						$aa1[$aa]="tyrosine";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "A"))
					{
						$aa1[$aa]="a stop codon";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "G")&&($seq1[$nt+2] eq "A"))
					{
						$aa1[$aa]="a stop codon";
					}
				elsif (($seq1[$nt] eq "T")&&($seq1[$nt+1] eq "A")&&($seq1[$nt+2] eq "G"))
					{
						$aa1[$aa]="a stop codon";
					}
				$nt+=3;
				$aa++;
			}
		$nt=1;
		$aa=1;
		while ($nt<=$length)
			{
				if (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "C"))
					{
						$aa2[$aa]="alanine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] ne "T"))
					{
						$aa2[$aa]="cysteine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] ne "C"))
					{
						$aa2[$aa]="cysteine";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] ne "C"))
					{
						$aa2[$aa]="aspartate";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] ne "T"))
					{
						$aa2[$aa]="aspartate";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] ne "G"))
					{
						$aa2[$aa]="glutamate";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] ne "A"))
					{
						$aa2[$aa]="glutamate";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "T")&&($seq2[$nt+2] ne "C"))
					{
						$aa2[$aa]="phenylalanine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "T")&&($seq2[$nt+2] ne "T"))
					{
						$aa2[$aa]="phenylalanine";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "G"))
					{
						$aa2[$aa]="glycine";
					}
				elsif (($seq2[$nt] eq "C")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] ne "C"))
					{
						$aa2[$aa]="histidine";
					}
				elsif (($seq2[$nt] eq "C")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] ne "T"))
					{
						$aa2[$aa]="histidine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "T")&&($seq2[$nt+2] ne "G"))
					{
						$aa2[$aa]="isoleucine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "A"))
					{
						$aa2[$aa]="lysine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "G"))
					{
						$aa2[$aa]="lysine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "T")&&($seq2[$nt+2] eq "G"))
					{
						$aa2[$aa]="leucine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "T")&&($seq2[$nt+2] eq "A"))
					{
						$aa2[$aa]="leucine";
					}
				elsif (($seq2[$nt] eq "C")&&($seq2[$nt+1] eq "T"))
					{
						$aa2[$aa]="leucine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "T")&&($seq2[$nt+2] eq "G"))
					{
						$aa2[$aa]="methionine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "C"))
					{
						$aa2[$aa]="asparagine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "T"))
					{
						$aa2[$aa]="asparagine";
					}
				elsif (($seq2[$nt] eq "C")&&($seq2[$nt+1] eq "C"))
					{
						$aa2[$aa]="proline";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "G"))
					{
						$aa2[$aa]="glutamine";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "A"))
					{
						$aa2[$aa]="glutamine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] eq "G"))
					{
						$aa2[$aa]="arginine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] eq "A"))
					{
						$aa2[$aa]="arginine";
					}
				elsif (($seq2[$nt] eq "C")&&($seq2[$nt+1] eq "G"))
					{
						$aa2[$aa]="arginine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] eq "T"))
					{
						$aa2[$aa]="serine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] eq "C"))
					{
						$aa2[$aa]="serine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "C"))
					{
						$aa2[$aa]="serine";
					}
				elsif (($seq2[$nt] eq "A")&&($seq2[$nt+1] eq "C"))
					{
						$aa2[$aa]="threonine";
					}
				elsif (($seq2[$nt] eq "G")&&($seq2[$nt+1] eq "T"))
					{
						$aa2[$aa]="valine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] eq "G"))
					{
						$aa2[$aa]="tryptophan";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "T"))
					{
						$aa2[$aa]="tyrosine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "C"))
					{
						$aa2[$aa]="tyrosine";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "A"))
					{
						$aa2[$aa]="a stop codon";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "G")&&($seq2[$nt+2] eq "A"))
					{
						$aa2[$aa]="a stop codon";
					}
				elsif (($seq2[$nt] eq "T")&&($seq2[$nt+1] eq "A")&&($seq2[$nt+2] eq "G"))
					{
						$aa2[$aa]="a stop codon";
					}
				$nt+=3;
				$aa++;
			}
		$nt=1;
		$aa=1;
		if ($identical==1)
			{
				print "The two sequences are identical.\n\n";
			}
		else
			{
				$mutationcounter=0;
				while ($nt<=$length)
					{
						$mutationcounter=0;
						if ($mutation[$nt]==1)
							{
								$mutationcounter++;
								$aa=($nt+2)/3;
							}
						if ($mutation[$nt+1]==1)
							{
								$mutationcounter++;
								$aa=($nt+2)/3;
							}
						if ($mutation[$nt+2]==1)
							{
								$mutationcounter++;
								$aa=($nt+2)/3;
							}
						if ($mutationcounter==1)
							{
								print "There is one ";
								if ($aa1[$aa] eq $aa2[$aa])
									{
										print "synonymous mutation in codon $aa.\n";
									}
								else
									{
										print "mutation in codon $aa which causes $aa2[$aa] to substitute $aa1[$aa].\n";
									}
							}
						elsif ($mutationcounter==2)
							{
								print "There are two ";
								if ($aa1[$aa] eq $aa2[$aa])
									{
										print "synonymous mutations in codon $aa.\n";
									}
								else
									{
										print "mutations in codon $aa which cause $aa2[$aa] to substitute $aa1[$aa].\n";
									}
							}
						elsif ($mutationcounter==3)
							{
								print "There are three mutations in codon $aa which cause $aa2[$aa] to substitute $aa1[$aa].\n";
							}
						$nt+=3;
					}
				print "\n";
			}
	}

Fixed a couple of errors, such as:

1. Restricted sequence length to numbers (previously you could enter letters or weird characters and it would interpret that as zero; you also can't choose zero as the sequence length anymore).
2. Fixed the verification thing (again, it didn't work well if you entered weird characters).

 

[BastardSonOfGod]

Well... I'm pretty sure I burned those programs on a Cd, but it must be in Chile too , I didn't continued creating programs because, since I came here, I spend almost all my time at work and the computer that I have here is not mine, so I can't install executable archives because is blocked , I only use my computer to chat.

Question: Wich program you use to compile in perl?

 

[Magrathean]

Well... I'm pretty sure I burned those programs on a Cd, but it must be in Chile too , I didn't continued creating programs because, since I came here, I spend almost all my time at work and the computer that I have here is not mine, so I can't install executable archives because is blocked , I only use my computer to chat.

That sucks, man. I hope you can get your own computer soon.

Question: Wich program you use to compile in perl?

TextWrangler 2.1.1. And i run them on the Mac Terminal.