#!/usr/bin/perl -w 

open(IF,"snyder_all.txt");
open(OF,">snyder_all.bed");
while($a=<IF>){
chomp($a);
($chrom,$start,$end,$strand,$gene) = split(/\t/,$a);
$chromhash{$gene} = "$chrom";
$strandhash{$gene} = "$strand";
print OF "$chrom\t$start\t$end\t$gene\t0\t$strand\n";
}
close(OF);
close(IF);
#chrI	130733	132084	+	YAL012W
#chrI	129237	130572	+	YAL013W

open(IF,"Gene_FeatureType_Introns.tsv");
open(OF,">GFTI_intron.bed");
while($a=<IF>){
chomp($a);
($gene,$start,$end) = split(/\t/,$a);
#YAL001C	151007	151096
if($chromhash{$gene} =~ /chrmt/){ 
#skip it
}
else{print OF "$chromhash{$gene}\t$start\t$end\tintron.$gene\t0\t$strandhash{$gene}\n";}
}

close(OF);
close(IF);