#!/usr/bin/perl -w 

use DBI; 

$db_user = "donohue"; 
$db_passwd = ""; 
$database = "DBI:mysql:one_sacCer3"; 
# remote database
# $database = "DBI:mysql:mm5_analysis;host=metarray.ucsc.edu;port=3306"; 
$mdb = DBI->connect($database, $db_user, $db_passwd) || die ("couldn't connect to database"); 

$cnt=0;
$q1uery = "select annName,alt_region,chrom,start,end,strand,type,start_pos,end_pos from clean_span ;";
$h1andle = $mdb->prepare($q1uery); 
$h1andle->execute; 
while( ($ann,$ar,$chrom,$justart,$juend,$strand,$type,$jusp,$juep) = $h1andle->fetchrow) {
#$pos = "$chrom:$justart-$juend";
$name = "$ann.$ar.$jusp.$juep";
if($justart+5<$juend){

system("twoBitToFa //gbdb/sacCer3/sacCer3.2bit:$chrom:$justart-$juend tmp.fa");
open(FA1 , "tmp.fa");
$fl=<FA1>;
$seqa = "";
while($fl=<FA1>){
	chomp($fl);
	$seqa .= "$fl" ;
}

$seqa =~ tr/a-z/A-Z/;
if($strand eq '-'){$tmp=reverse($seqa);$tmp=~ tr/ACTG/TGAC/;$seqa=$tmp;}
print ">$name\n";
print "$seqa\n";


}
}