#Reference Francis
#use warnings;
use XML::Simple;
use LWP::UserAgent;
use HTTP::Request::Common;
use URI::Escape;
use Data::Dumper;
use Text::CSV;
use List::Util qw( min max );


my @protein_keywords = ("inhibitors", "inhibitor", "activity", "activitor", "activities", "activated", "proteins", "deficiency", "levels", "functions", "reductions", "protease", "proteases", "complex concentrate");

my $ua = LWP::UserAgent->new;
my $csv = Text::CSV->new({ sep_char => ',' });
my $ab_csv = Text::CSV->new({ sep_char => ',' });

#Open result CSV file.
open(my $fh, ">", "output1.csv");
print $fh "Pubmed ID, Drug Name, Position of keywords, Valid Proteins, Position of proteins, Minimum separation, Scoring\n";


#open abnormal condition csv file
my $i = 0;
my @protein_list;
open(my $abnorm, '<', "Protein.csv");
while (my $ab_line = <$abnorm>) {
	chomp $ab_line;

	if ($ab_csv->parse($ab_line))
	{
		#skip first line
		next if ($. == 1);

		my @ab_fields = $ab_csv->fields();
		$protein_list[$i] = $ab_fields[0].$ab_fields[1];
		$i++;
	
	}
}

#Open specified CSV file
open(my $data, '<', "finalidlist.csv");
while (my $line = <$data>) 
{
	chomp $line;

	if ($csv->parse($line)) 
	{
		#Skip first line
		next if ($. == 1);
	}
	
   		my @fields = $csv->fields();
   		my $valid_proteins = "";

   		push my @id , $fields[1];
   		foreach my $id(@id){
   			if ($id ne "no"){
 
		#Initialize http request
		my $args = "db=pubmed&id=$id&retmode=text&rettype=abstract";
		my $req = new HTTP::Request POST => 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi';
		$req->content_type('application/x-www-form-urlencoded');
		$req->content($args);
	
		#Get response
		my $response = $ua->request($req);
		my $content = $response->content;
		#$content = lc($content);

		my @abstract = split /[.]/, $content;

		my $keyword_position = "";
		foreach my $protein_keywords(@protein_keywords) {
			my $i = 0;
			foreach my $abstract (@abstract){
			if($abstract =~ /\b$protein_keywords\b/i)
			{
				$keyword_position = $keyword_position . "+" . $i;
				$i++;
			}
			else
			{
				$i++;
			}
		}}


		foreach my $protein_list(@protein_list) {
			my @each_protein_list = split/[+]/, $protein_list; 

			my $i = 0;
			my $protein_position = "";
			foreach my $abstract(@abstract){
				my @tempt = split /[,]/, $abstract;
				foreach my $each_protein(@each_protein_list)
				{
					if ($each_protein eq "\U$each_protein"){
						$each_protein = uc $each_protein;
					}

					foreach	my $tempt(@tempt){			#yo tempt wala loop chai , wala kura separate garnalai ho hai but problem solve vako xaina
					if($tempt =~ /\b$each_protein\b/i)	#main modify garne thau yo ho ..match navayara tanaab diyako xa
					{
							$valid_proteins = $each_protein;
						
			
						 #print $tempt;
						 #print "\n";
						 #print $each_protein;
						 #print "\n";
						$protein_position = $protein_position . "+" . $i;
					}}
				}
				$i++;
			}

			if($protein_position ne "")
			{
				my $field2 = $keyword_position;
				my $field3 = $protein_position;
			
				my @keywords = split /[+]/, $keyword_position;
				splice (@keywords, 0, 1);
			
				my @proteins = split /[+]/, $protein_position;
				splice (@proteins, 0, 1);

				sub uniq {
    				my %seen;
    				grep !$seen{$_}++, @_;
				}

				@proteins = uniq(@proteins);
				
				my @temp;
				my $f = 0;
				foreach my $proteins(@proteins){
					my $k = 0;
					my @difference;
					foreach my $keywords(@keywords)
					{
						my $diff = ($proteins - $keywords);
						$difference[$k] = abs $diff;
						$k++;
					}
					$temp[$f] = min @difference;
					$f++;
				}

				my $min = min @temp;

				if($min == 0)
				{
					print "$valid_proteins\n";
					$scoring = 1;
					print $fh "$fields[1], $fields[0], $field2, $valid_proteins, $field3, $min, $scoring\n";
					print "$fields[1], $fields[0], $field2, $valid_proteins, $field3, $min, $scoring\n";

				}
				elsif($min == 1)
				{
					print "not matched\n";
					$scoring = 0.5;
					print $fh "$fields[0], $fields[0], $field2, Unmatched proteins, $field3, $min, $scoring\n";
					print "$fields[0], $fields[0], $field2, Unmatched proteins, $field3, $min, $scoring\n";
				}
				else
				{
					print "not matched\n";
					$scoring = 0.2;
					print $fh "$fields[1], $fields[0] $field2, Unmatched proteins, $field3, $min, $scoring\n";
					print "$fields[1], $fields[0] $field2, Unmatched proteins, $field3, $min, $scoring\n";
				}



				#print $fh "$fields[0], $field2, $protein_list, $field3, $min, $scoring\n";
			
			}
		}	
	}
	
	else
	{
		print "not matched\n";
		$scoring = 0;
		print $fh "Undef, $fields[0] $field2, Unmatched proteins, $field3, $min, $scoring\n";
		print "Undef, $fields[0] $field2, Unmatched proteins, $field3, $min, $scoring\n";

	}
	}
	

}

close($fh);