#!usr/bin/perl -w

### Takes Genbank file, extracts DNA sequence, formats and spits out FASTA file. ###

use strict;
use library;

my @annotation = ();
my $sequence = '';
my $definition = '';
my $definition_flag = 0;

my $filename = usrquery ("Please enter genbank filename");

parse1 (\@annotation, \$sequence, $filename);

$sequence =~ tr/actg/ACTG/;

foreach my $element (@annotation)
	{if ($element =~ /^DEFINITION/)
		{$element =~ s/^DEFINITION\s*//;
		$definition = $element;
		$definition_flag = 1;}
	elsif ($element =~ /^ACCESSION/)
		{$element =~ s/^ACCESSION\s*//;
		$definition_flag = 0;}
	elsif ($definition_flag)
		{chomp ($definition);
		$element =~ s/^\s*/ /;
		$definition .= $element;}
		}

print "\nPlease enter filename for outfile.\n\n";
my $outputfile = <STDIN>;
chomp $outputfile;
unless 	(open(OUTFILE, ">$outputfile"))
	{print "Cannot open file \"OUTFILE\" to write to";
	exit;}
print OUTFILE ">$definition";
print OUTFILE "$sequence\n";
close (OUTFILE);


exit;

############################################################

sub parse1	
{my ($annotation, $dna, $filename)= @_;
my $in_sequence_flag = 0;
my @genbankfile = ();
@genbankfile = read_file_data ($filename);

foreach my $line (@genbankfile)
	{if ($line =~ /^\/\/\n/)
		{last;}
	elsif ($in_sequence_flag) 
		{$sequence .= $line;}
	elsif ($line =~ /^ORIGIN/)
		{$in_sequence_flag = 1;}
	else 
		{push (@annotation, $line);}
	}

$sequence =~ s/[\s0-9]//g;

}