#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", "activi
+tor", "activities", "activated", "proteins", "deficiency", "levels", 
+"functions", "reductions", "protease", "proteases", "complex concentr
+ate");

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, ">", "Result1.csv");
print $fh "Pubmed ID, Position of keywords, Valid proteins, Position o
+f 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, '<', "publist.csv");
while (my $line = <$data>) 
{
    chomp $line;

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

        #Initialize http request
        my $args = "db=pubmed&id=$fields[0]&retmode=text&rettype=abstr
+act";
        my $req = new HTTP::Request POST => 'https://eutils.ncbi.nlm.n
+ih.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)
                {
                    $each_protein = lc($each_protein);   

                    foreach    my $tempt(@tempt){            #yo tempt
+ wala loop chai , wala kura separate garnalai ho hai but problem solv
+e vako xaina
                    if($tempt =~ /\b$each_protein\b/i)    #main modify
+ garne thau yo ho ..match navayara tanaab diyako xa
                    {
                         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)
                {
                    $scoring = 1;
                    my $valid_protein = $each_protein;
    
                }
                elsif($min == 1)
                {
                    $scoring = 0.5;
                }
                else
                {
                    $scoring = 0.2;
                }


                print $fh "$fields[0], $field2, $valid_protein, $field
+3, $min, $scoring\n";
            }
        }
    
    }

}
close($fh);
[download]

Hello monks! This is the code I am using to list the protein names in the abstract if the protein names are followed by the keywords listed in @protein_keywords in the above code. I get data on every field of the resulting CSV file but the field "valid_protein" is empty. Can anyone suggest me what is the reason behind this?