print "\nWelcome to the FASTA to QUASI converter.\n";

print "\nRemember that the sequences must be aligned and that the\n";

print '"no data" symbol: "." is distinct from the true alignment gap symbol: "-"';

print "\n";



#gets the names of the files and opens them

print "Enter the name of the FASTA file to convert:\n";

chomp($infile_name = <STDIN>);

open(INFILE,"$infile_name");

print "\nEnter the name you want for the converted QUASI-ready output file:\n";

chomp($outfile_name = <STDIN>);

open(OUTFILE,">$outfile_name");



$status="start";



while (eof(INFILE) == 0) {

	$fromin=getc(INFILE);

	$seqletter = "";



	if ($status eq "start" && $fromin eq ">") {

		#once the first name starts, I stop ignoring garbage

		$status = "name";

		}

	#next I check for the FASTA name and ignore it until it's finished.

	if ($status eq "name" && $fromin eq "\n") {

		#now we know we are in the sequence section

		$status = "sequence";

		}

	#Now, Ihave to check once again for the beginning of a new name (and

	#I will output a newline if there is a name (i.e., the sequence is finished)

	if ($status eq "sequence" && $fromin eq ">") {

		$status = "name";

		print OUTFILE ("\n");

		}

	#Next I read only the valid symbols into the seq var

	if ($status eq "sequence") {

		#standard nucleotides are allowed

		if ($fromin eq "a" || $fromin eq "A") {

			$seqletter = "A";

			}

		if ($fromin eq "c" || $fromin eq "C") {

			$seqletter = "C";

			}

		if ($fromin eq "d" || $fromin eq "D") {

			$seqletter = "D";

			}

		if ($fromin eq "e" || $fromin eq "E") {

			$seqletter = "E";

			}

		if ($fromin eq "f" || $fromin eq "F") {

			$seqletter = "F";

			}

		if ($fromin eq "g" || $fromin eq "G") {

			$seqletter = "G";

			}

		if ($fromin eq "h" || $fromin eq "H") {

			$seqletter = "H";

			}

		if ($fromin eq "I" || $fromin eq "i") {

			$seqletter = "I";

			}

		if ($fromin eq "K" || $fromin eq "k") {

			$seqletter = "K";

			}

		if ($fromin eq "L" || $fromin eq "l") {

			$seqletter = "L";

			}

		if ($fromin eq "m" || $fromin eq "M") {

			$seqletter = "M";

			}

		if ($fromin eq "n" || $fromin eq "N") {

			$seqletter = "N";

			}

		if ($fromin eq "p" || $fromin eq "P") {

			$seqletter = "P";

			}

		if ($fromin eq "q" || $fromin eq "Q") {

			$seqletter = "Q";

			}

		if ($fromin eq "r" || $fromin eq "R") {

			$seqletter = "R";

			}

		if ($fromin eq "S" || $fromin eq "s") {

			$seqletter = "S";

			}

		if ($fromin eq "t" || $fromin eq "T") {

			$seqletter = "T";

			}

		if ($fromin eq "V" || $fromin eq "v") {

			$seqletter = "V";

			}

		if ($fromin eq "W" || $fromin eq "W") {

			$seqletter = "W";

			}

		if ($fromin eq "x" || $fromin eq "X") {

			$seqletter = "X";

			}

		if ($fromin eq "y" || $fromin eq "Y") {

			$seqletter = "Y";

			}



		#now the gap and no data symbols are allowed

		if ($fromin eq "-") {

			$seqletter = "-";

			}

		if ($fromin eq ".") {

			$seqletter = ".";

			}

		}

	#Finally, we will print the letter

	unless ($seqletter eq "") {

		print OUTFILE ("$seqletter");

		}

	}

		

close(INFILE);

close(OUTFILE);