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use strict;
use Bio::SeqIO;
use LWP::Simple;

my $iCnt = 0;
# URLs for target files. qw --> no need to use quatation marks.
my @aUrls = qw (
	http://lab.gutdesigner.com/research_perl_data/AGRI01.1.gbk
	http://lab.gutdesigner.com/research_perl_data/ASJE01.1.gbk
	http://lab.gutdesigner.com/research_perl_data/AVAQ01.1.gbk
);

my $sDownFolder = "Download_GenBank";
system("mkdir ".$sDownFolder);
print "--------------------------------------------\n";
foreach my $sCurUrl (@aUrls) {
	$iCnt++;
	my $sLocalFile = $sDownFolder."/".funcFileNameFromPath($sCurUrl);
	print "Target ".$iCnt."\t".$sLocalFile."\n";

	my $oRespond = getstore($sCurUrl, $sLocalFile);    # If a url is not correct, no exception occurs.
	if (is_error($oRespond)) {
		print "    Downloading failed: ".$sCurUrl."\n";
		print "    Error Message: ".$oRespond."\n";
	}
}

sub funcFileNameFromPath {
	my $sFilePath = shift;
	my $sRevPath = reverse($sFilePath);
	my $sFileName = "";

	if ($sRevPath=~/\//){
		$sFileName = $`;
		$sFileName = reverse($sFileName);
	} else {
		$sFileName = $sFilePath;
	}
	return $sFileName;
}





# Loading each GenBank file one by one
my @aGenBankFiles = glob($sDownFolder."/*.gbk");
$iCnt = 0;

print "--------------------------------------------\n";
foreach my $sCurGbFile (@aGenBankFiles) {
	$iCnt++;
	my $sCnt = sprintf("%04d",$iCnt);
	print "Processing ".$iCnt.": ".$sCurGbFile."\n";
	funcGenBankProcessing($sCurGbFile, $sDownFolder);
} 
print "--------------------------------------------\n";
print "Finished!!\n";



sub funcGenBankProcessing {
	my $sGenBankFile = shift;
	my $sSaveFolder  = shift;
	my $sSaveFile    = $sSaveFolder."/".funcFileNameFromPath($sGenBankFile)."_Table.txt";

	open (hOut, ">".$sSaveFile) or die;
	print "    Saving: ".$sSaveFile."\n";
	my $oGbk = Bio::SeqIO->new(-file => $sGenBankFile, -format => 'genbank');

	print hOut "Strains"        ."\t";
	print hOut "Seq_IDs"        ."\t";
	print hOut "Description"    ."\t";
	print hOut "F\/R"           ."\t";
	print hOut "Symbols"        ."\t";
	print hOut "Products"       ."\t";
	print hOut "Protein_IDs"    ."\t";
	print hOut "A.A"            ."\t";
	print hOut "CDS_Length(bp)" ."\t";
	print hOut "DNA_Seq"        ."\t";
	print hOut "X_Ref"          ."\n";

	while(my $oSeq = $oGbk->next_seq()) {
		my @aStrain  = ();
		my $sCdsInfo = "";
		my $sSeqId   = "";
		my $sSeqdesc = "";

		foreach my $oCurFeat ( $oSeq->get_SeqFeatures() ) {
			# Get the Strain information
			if ($oCurFeat->primary_tag eq "source") {    
				##############################################################
				eval {
					@aStrain = $oCurFeat->get_tag_values("strain");
				};
				if ($@) {
					print $@."\n";
					if ($@ =~ m/asking for tag value that does not exist/) {
						$aStrain[0] = "None";			
					}
				}
			}

			# Get a sequence ID for this sequence
			eval {
				$sSeqId = $oSeq->display_id();
			};
			if ($@) {
				if ($@ =~ m/asking for tag value that does not exist/) {
					$sSeqId = "None";
				}
			}

			# Get a sequence description for this sequence
			eval {
				$sSeqdesc = $oSeq->desc();
			};
			if ($@) {
				if ($@ =~ m/asking for tag value that does not exist/) {
					$sSeqdesc = "None";
				}
			}


			# Get each CDS information
			if ($oCurFeat->primary_tag eq "CDS") {
				$sCdsInfo = "";

				my $sSeqFinal     = "";
				my $sOrient       = "";
				my @aGeneName     = ();
				my @aProduct      = ();
				my @aProtId       = ();
				my @aAminoAcid    = ();
				my @aDbXrefs      = ();

				# Get a sequence for this CDS
				$sSeqFinal        = $oSeq->subseq($oCurFeat->start, $oCurFeat->end);
				if ($oCurFeat->strand == 1) {
					$sOrient = "+";
				} else {
					$sOrient = "-";
					$sSeqFinal = funcRevComp($sSeqFinal);
				}

				# Get a gene symbol or gene name for this CDS
				eval {	
					@aGeneName = $oCurFeat->get_tag_values("gene");
				};
				if ($@) {
					if ($@ =~ m/asking for tag value that does not exist/) {
						$aGeneName[0]="None";
					}
				}

				# Get a product name for this CDS
				eval {
					@aProduct = $oCurFeat->get_tag_values("product");
				};
				if ($@) {
					if ($@ =~ m/asking for tag value that does not exist/) {
						$aProduct[0]="None";
					}
				}

				# Get a protein ID for this CDS
				eval {#protein number id : 
					@aProtId = $oCurFeat->get_tag_values("protein_id");
				};
				if ($@) {
					if ($@ =~ m/asking for tag value that does not exist/) {
						$aProtId[0]="None";
					}
				}

				# Get an amino acid sequence for this CDS
				eval {
					@aAminoAcid	= $oCurFeat->get_tag_values("translation");
				};
				if ($@) {
					if ($@ =~ m/asking for tag value that does not exist/) {
						$aAminoAcid[0]="None";
					}
				}

				# Get external database IDs for this CDS
				eval {
					@aDbXrefs = $oCurFeat->get_tag_values("db_xref");
				};
				if ($@) {
					if ($@ =~ m/asking for tag value that does not exist/) {
						$aDbXrefs[0]="None";
					}
				}
				my $sDbXrefs = join(" \/ ", @aDbXrefs);

				$sCdsInfo = $sCdsInfo.$aStrain[0]        ."\t";
				$sCdsInfo = $sCdsInfo.$sSeqId            ."\t";
				$sCdsInfo = $sCdsInfo.$sSeqdesc          ."\t";
				$sCdsInfo = $sCdsInfo.$sOrient           ."\t";
				$sCdsInfo = $sCdsInfo.$aGeneName[0]      ."\t";
				$sCdsInfo = $sCdsInfo.$aProduct[0]       ."\t";
				$sCdsInfo = $sCdsInfo.$aProtId[0]        ."\t";
				$sCdsInfo = $sCdsInfo.$aAminoAcid[0]     ."\t";
				$sCdsInfo = $sCdsInfo.length($sSeqFinal) ."\t";
				$sCdsInfo = $sCdsInfo.$sSeqFinal         ."\t";
				$sCdsInfo = $sCdsInfo.$sDbXrefs;

				print hOut $sCdsInfo."\n";
			}
		}
	}
	close(hOut);
}

sub funcRevComp {
	my $sSeq = reverse uc($_[0]);
	$sSeq =~ tr/ATGCN/TACGN/;                     # A -> T, T ->A, G -> C, C -> G, N -> N
	return $sSeq;	
}



# For more information, refer to the following link
# https://www.tutorialspoint.com/perl
# https://metacpan.org/pod/Bio::DB::GenBank