Get gene start and end from GTF file

In a GTF file that does not have CDS records annotated, its tricky to get the start and end coordinates of a gene. This script does just that and prints a nice BED format file. It also report the genes that occur on multiple scaffolds or chromosomes as errors. These can be greped out using grep -v "Error".

 #!/usr/bin/perl  
 my $gtf1 = $ARGV[0];  
 my %scaf=();  
 my $start=();  
 my %end=();  
 my %multi=();  
 open(GTF1, $gtf1);  
 while($z=<GTF1>){   
 chomp $z;  
 my @parts=split(/\t/,$z);  
 my $start=$parts[3];  
 my $end=$parts[4];  
 my @parts2=split(/\s/,$parts[8]);  
 my $gene=$parts2[1];  
 $gene=~s/[\;\"]//g;  
 ##print "$gene\t$start\t$end\n";  
 if(!(exists $scaf{$gene})){$scaf{$gene}=$parts[0];}  
 elsif(!($scaf{$gene}=~m/$parts[0]/)){$multi{$gene}=1;}  
 if(!(exists $start{$gene})){$start{$gene}=$start;$end{$gene}=$end;}  
 else{$end{$gene}=$end;}  
 }  
 close(GTF1);  
 foreach my $keygene(sort keys %scaf){  
 if($start{$keygene}>$end{$keygene}){$temp=$start{$keygene};$start{$keygene}=$end{$keygene};$end{$keygene}=$temp;}  
 if(!(exists $multi{$keygene})){print "$scaf{$keygene}\t$start{$keygene}\t$end{$keygene}\t$keygene\n";}  
 else{print "Error:Gene $keygene on mutiple scaffolds\n";}  
 }