#!usr/bin/perl 

### Script reads in sequence file, formats sequence and creates
# formatted output file, with subset of sequence defined by user.

use strict;
use library;

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

my @filedata = read_file_data ($filename);
my $tag = extract_tag (@filedata);
my $sequence = extract_sequence (@filedata);
$sequence =~ tr/actg/ACTG/;
composition ($sequence);

#start loop
do {

my $pos1;
my $pos2;
my $start = usrquery ("Please enter start position (or space to quit)");

if ($start =~ /^\s*$/)
		{exit;}

my $stop = usrquery ("Please enter stop position");

if ($start > $stop) 	
	{$pos1 = $stop;
	$pos2 = $start;			
	}
else 	{$pos1 = $start;
	$pos2 = $stop;
	}

my $length = abs ($pos2 - $pos1);

my $sub_sequence = substr ($sequence, ($pos1-1), $length);

my $outputfile = usrquery ("Please enter output filename");
unless 	(open(OUTFILE, ">$outputfile"))
	{print "Cannot open file \"OUTFILE\" to write to";
	exit;}

print OUTFILE "$tag, positions $pos1 to $pos2.\n";
print OUTFILE $sub_sequence;
close OUTFILE;

#close loop
} 
until (my $start =~ /quit/ );

exit;