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use strict;
use LWP::Simple;

my $iCnt = 0;
# URLs for target files. qw --> no need to use quatation marks.
my @aUrls = qw (
	ftp://ftp.ncbi.nlm.nih.gov/sra/wgs_aux/AZ/FR/AZFR01/AZFR01.1.fsa_nt.gzz
	ftp://ftp.ncbi.nlm.nih.gov/sra/wgs_aux/AV/AI/AVAI01/AVAI01.1.fsa_nt.gz
	ftp://ftp.ncbi.nlm.nih.gov/sra/wgs_aux/AX/DQ/AXDQ01/AXDQ01.1.fsa_nt.gz
);

my $sDownFolder = "Download_WGS";
system("mkdir ".$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;
}





# Prokaryotic Nomenclature - Database
# https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloads.html
# https://www.dsmz.de/fileadmin/Bereiche/ChiefEditors/BacterialNomenclature/DSMZ_bactnames.xlsx

my $sUrl = "http://lab.gutdesigner.com/research_perl_data/ProkaryotesNames.txt";
my $sSaveFile = "ProkaryotesNames.txt";
getstore($sUrl, $sSaveFile);                    # If a url is not correct, no exception occurs.

print "--------------------------------------------\n";
print "Target URL: ".$sUrl."\n";
if (-f $sSaveFile) {                            # If the file exists
	print "Downloaded File:".$sSaveFile."\n";
}
print "\n";


# Open the file and count the number of genus
my %hGenus_by_Genus = ();
open (hIn, $sSaveFile) or die;
<hIn>;                                          # Read the first line and do not use it.
while (my $sLine = <hIn>) {
	$sLine =~s/\n//g;
	$sLine =~s/\r//g;

	my @aLine = split("\t", $sLine);
	my $sCurGenus = $aLine[0];
	$hGenus_by_Genus{$sCurGenus} = $sCurGenus;
}
close(hIn);

my @aGenusNames = keys(%hGenus_by_Genus);
my $iGenusCnt = 0;
print "--------------------------------------------\n";
foreach my $sCurGenus (@aGenusNames) {
	$iGenusCnt++;
	if ($iGenusCnt <= 20) {
		printf("%-2s %-20s\n", $iGenusCnt, $sCurGenus);
	}
}
print "-----------------------------------\n";
print "The number of Genera: ".$iGenusCnt."\n";

print "--------------------------------------------\n";
$iGenusCnt = 0;
@aGenusNames = sort {$a cmp $b} @aGenusNames;  # Sorting lexically
foreach my $sCurGenus (@aGenusNames) {
	$iGenusCnt++;
	if ($iGenusCnt <= 20) {
		printf("%-2s %-20s\n", $iGenusCnt, $sCurGenus);
	}
}
print "-----------------------------------\n";
print "The number of Genera: ".$iGenusCnt."\n";



# Open the file and count the number of species
my %hBiName_by_BiName = ();
open (hIn, $sSaveFile) or die;
<hIn>;                                          # Read the first line and do not use it.
while (my $sLine = <hIn>) {
	$sLine =~s/\n//g;
	$sLine =~s/\r//g;

	my @aLine = split("\t", $sLine);
	my $sCurGenus = $aLine[0];
	my $sCurSpec  = $aLine[1];
	if ($sCurSpec eq "") {
		next;
	} else {
		my $sCurBiName = $sCurGenus." ".$sCurSpec;
		$hBiName_by_BiName{$sCurBiName} = $sCurBiName;
	}
}
close(hIn);

print "--------------------------------------------\n";
my $iBiNameCnt = 0;
my @aBiNames = keys(%hBiName_by_BiName);
@aBiNames = sort {$a cmp $b} @aBiNames;  # Sorting lexically
foreach my $sCurBiName (@aBiNames) {
	$iBiNameCnt++;
	if ($iBiNameCnt <= 20) {
		printf("%-2s %-20s\n", $iBiNameCnt, $sCurBiName);
	}
}
print "-----------------------------------\n";
print "The number of Genera: ".$iBiNameCnt."\n";


# For more information, refer to the following link
# https://www.tutorialspoint.com/perl