# This is part of the parser for NCBI RefSeq data 
while(<DATA>){
	chomp;	
	if(/^>gi\|(\d+)\|ref\|([\w\_\.]+)\|/){
		$locus = $2;
		$seq{$locus} = "" ;		
	  $GI{$locus} = $1 ;
	}
	else{
		$seq{$locus} = $seq{$locus}.$_ ;
	}
}
close DATA;

<In_Gene2refseq> ;
while(<In_Gene2refseq>){
	chomp;
	@array = split(/\t/,$_) ;
	if( exists($seq{$array[5]}) ){
		$gi2gene{$array[5]} = $array[1] ; 
		$gene2gi{$array[1]} = $array[5] ;
		if( $array[12]=~/Reference assembly/ and $array[7]=~/NC_/ ){			
			$START{$array[1]} = $array[9] ;  
			$END{$array[1]} = $array[10] ;    
			$ORIENT{$array[1]} = $array[11] ; 
		}
	}
}
close(In_Gene2refseq);

<In_GeneInfo> ;
while(<In_GeneInfo>){
	chomp;
	@array = split(/\t/,$_) ;
	if( exists($gene2gi{$array[1]}) ){
		$GN{$array[1]} = $array[2] ;
		$array[4] =~s/\|/@/g ;
		$GS{$array[1]} = $array[4] ;		
		$DE{$array[1]} = $array[8] ;
		$CHR{$array[1]} = $array[6];
	}
}
close(In_GeneInfo);

# From KEGG Gene ID to KEGG Pathway
while(<In_PATH>){
	chomp;
	@array = split(/\t/,$_);
	$array[1] =~s/path:// ;
	if( !exists($KEGG_path{$array[0]}) ){
		$KEGG_path{$array[0]} = $array[1] ;
	}
	else{
		$KEGG_path{$array[0]} = $KEGG_path{$array[0]}.";".$array[1]  ;
	}
}
close(In_PATH);

# From NCBI GI to KEGG Gene ID
while(<In_KEGG>){
	chomp;
	@array = split(/\t/,$_) ;
	$array[1] =~s/ncbi-gi:// ;
	if( !exists($KEGG_path{$array[0]}) ){
		$KEGG_path{$array[0]} = "NA" ;
	}
	$KEGG{$array[1]} = $array[0]."\t".$KEGG_path{$array[0]} ;
}
close(In_KEGG);

# From NCBI Gene ID to GO
<In_GO>;
while(<In_GO>){
	chomp;
	@array = split(/\t/,$_);
	if( exists($gene2gi{$array[1]}) ){
		if($array[7] eq "Function"){
			if( !exists($go{$array[1]}) ){
				$go{$array[1]} = $array[2]."@".$array[3]."@"."MF" ;
			}
			else{
				$go{$array[1]} = $go{$array[1]}.";".$array[2]."@".$array[3]."@"."MF" ;
			}
		}
		elsif($array[7] eq "Component"){
			if( !exists($go{$array[1]}) ){
				$go{$array[1]} = $array[2]."@".$array[3]."@"."CC" ;
			}
			else{
				$go{$array[1]} = $go{$array[1]}.";".$array[2]."@".$array[3]."@"."CC" ;
			}
		}
		elsif($array[7] eq "Process"){
			if( !exists($go{$array[1]}) ){
				$go{$array[1]} = $array[2]."@".$array[3]."@"."BP" ;
			}
			else{
				$go{$array[1]} = $go{$array[1]}.";".$array[2]."@".$array[3]."@"."BP" ;
			}
		}
	}
}
close(In_GO);

print OUT "GI", "\t", "REFSEQ", "\t", "SQ", "\t", "GENEID", "\t", 
"CHR", "\t", "START", "\t", "END", "\t", "ORIENT", "\t", 
"GN", "\t", "SYMBOL", "\t", "DE", "\t", "KEGG", "\t", "PATH", "\t", 
"GO", "\n" ;  

@locus = sort(keys(%seq)) ; 
foreach $locus(@locus){	
	if( !exists($gi2gene{$locus}) ){
		$GeneID = "NA" ;
	}
	else{
		$GeneID = $gi2gene{$locus} ;
	}
	if( !exists($RefSeq{$GeneID}) ){
		$RefSeq{$GeneID} = "NA" ;	
	}
	if( !exists($CHR{$GeneID}) ){
		$CHR{$GeneID} = "NA" ;
	}
	if( !exists($START{$GeneID}) ){
		$START{$GeneID} = "NA";
	}
	if( !exists($END{$GeneID}) ){
		$END{$GeneID} = "NA";
	}
	if( !exists($ORIENT{$GeneID}) ){
		$ORIENT{$GeneID} = "NA"; 
	}
	if( !exists($GN{$GeneID}) ){
		$GN{$GeneID} = "NA" ;
	}
	if( !exists($GS{$GeneID}) ){
		$GS{$GeneID} = "NA" ;
	}
	if( !exists($DE{$GeneID}) ){
		$DE{$GeneID} = "NA" ;
	}
	if( !exists($KEGG{$GI{$locus}}) ){
		$KEGG{$GI{$locus}} = "NA\tNA" ;
	}
	if( !exists($go{$GeneID}) ){
		$go{$GeneID} = "NA" ;
	}
	print OUT "$GI{$locus}\t$locus\t$seq{$locus}\t$GeneID\t$CHR{$GeneID}\t$START{$GeneID}\t$END{$GeneID}\t$ORIENT{$GeneID}\t$GN{$GeneID}\t$GS{$GeneID}\t$DE{$GeneID}\t$KEGG{$GI{$locus}}\t$go{$GeneID}\n" ;
}
close OUT;