#!/usr/local/bin/perl
# raw2fa.pl

use lib('/bio/work/meow/');
use euGenes::GenomeFeatures;
use Getopt::Long;    

my $workpath= '/c7/eugenes/genomew/';  
my @csome=();
my $subrange='';

$usage= <<USAGE;
$0 -- convert raw sequence file to fasta format
options:
'workpath=s' => $workpath,
'org=s' => $org,         -- input org & csome(s)
'csomes=s' => @csome,
'dnafile=s' => $dnafile, -- OR input dnafile
'subrange=s' => $subrange,  -- null or subrange to extract
'debug!' => $debug,
'reverse!' => $reverse,

USAGE
#'outpath=s' => $outpath,
#'run!' => $dorun,

GetOptions( 
'dnafile=s' => \$dnafile,
'subrange=s' => \$subrange,
'workpath=s' => \$workpath,
'org=s' => \$org,
'csomes=s' => \@csome,
'debug!' => \$debug,
'reverse!' => \$reverse,
);

die $usage unless($dnafile || (@csome && $org));
#'outpath=s' => \$outpath,
#'run!' => \$dorun,

my $gnofeats= euGenes::GenomeFeatures->new( 
	org => $org,
	workpath => $workpath,
	dnafile => $dnafile,
	);

## test reverse
if ($reverse) {
	local(*F); 
	unless(open(F,$dnafile)) { warn "Can't open $dnafile"; return; }
	my ($len, $nr, $data); 
	seek(F, 0, 2);
	$len= tell(F);
	seek(F, 0, 0);
	$n= read(F,$data,$len);
	print STDERR "read $n from $dnafile:\n";
	print STDERR substr($data,0,75),"...\n";
	print STDERR substr($data,$len-75,75),"\n";
	print STDERR "start reverse...\n";
	$revd= reverse $data;
	print STDERR "done reverse...\n";
	print STDERR substr($revd,0,75),"...\n";
	print STDERR substr($revd,$len-75,75),"\n";
	exit;
	}
	
## or $ens->init( ... );
if (@csome) {
	foreach $csome (@csome) {
		$gnofeats->init(
			org => $org,
			chromosome => $csome,
			);
		$gnofeats->raw2fasta($dnafile,$subrange); 
		}
	}
else {
	$gnofeats->raw2fasta($dnafile,$subrange); 
	}