#!/usr/bin/perl


####################################################

# This program has been written by Biju Issac for
# extracting cds from genbank files

####################################################


$cnt=0;
open(FO,">$ARGV[1]");
open(FL,"$ARGV[0]"); #open combined features file
while($line=<FL>){
    chomp($line);
    @cod=split(/\s+/,$line);
    if($cod[0] eq "LOCUS"){
	if($cnt>0){
	    $cds=~s/[^0-9]/ /g;
	    $cds=~s/\s+/ /g;
	    print FO "$name $cds\n";
	}
	$cnt++;
	$name="$cod[1]";$s=0;$cds="";
    }
    if($cod[1] eq "CDS"){
	$s=1;$cds="";
    }
    if($s==1){
	$gim=substr($cod[1],1,4);
	if($gim eq "gene" || $gim eq "tran" ||  $gim eq "db_x" || $gim eq "codo" || $gim eq "EC_n" || $gim eq "prod" || $gim eq "note"){
	    $s=0;
	}
    }
    if($s==1){
	for($i=1;$i<@cod;$i++){
	    $cds.=" $cod[$i]";
	}
    }
}
if($cnt>0){
    $cds=~s/[^0-9]/ /g;
    $cds=~s/\s+/ /g;
    print FO "$name $cds\n";
}
close FL;
close FO;