#!/usr/bin/perl -w 

open(IF,"ares_sc3_isoformst.bed");
while($a=<IF>){
chomp($a);
#chrI	87285	87752	SNC1	0	+	87285	87752	0	2	102,252,	0,215,
@b=split(/\t/,$a);
$n=$b[9];
$chrom=$b[0];
if($n>1){

@sizes = split(/,/,$b[10]);
@starts = split(/,/,$b[11]);
for($i=0;$i<$n;$i++){
$tstart = $b[1] + $starts[$i];
$tend = $tstart + $sizes[$i];
$bedhash{"$chrom $tstart $tend"}= $b[3];
print "$chrom $tstart $tend\n";
}
}}


print "<pre>\n";

open(POS,">allpos.bed");
open(NEG,">allneg.bed");

use DBI; 

$db_user = "donohue"; 
$db_passwd = ""; 
$database = "DBI:mysql:one_sacCer3"; 
$mdb = DBI->connect($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<$juend){
if($strand eq '+') {print POS "$chrom\t$justart\t$juend\t$name\t0\t$strand\n";}
else{print NEG "$chrom\t$justart\t$juend\t$name\t0\t$strand\n";}
}


#log2((INa x EXb)/(INb x EX a))  (for IAI)

}