#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, ">", "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.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 $each_protein(@each_protein_list)
                {
                    if ($each_protein eq "\U$each_protein"){
                        $each_protein = uc $each_protein;
                    }

                    foreach    my $tempt(@tempt){            #yo tempt
+ wala loop chai , wala kura separate garnalai ho hai but problem solv
+e vako xaina
                    if($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_pro
+teins, $field3, $min, $scoring\n";

                }
                elsif($min == 1)
                {
                    print "not matched\n";
                    $scoring = 0.5;
                    print $fh "$fields[0], $fields[0], $field2, Unmatc
+hed 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, Unmatch
+ed proteins, $field3, $min, $scoring\n";
                    print "$fields[1], $fields[0] $field2, Unmatched p
+roteins, $field3, $min, $scoring\n";
                }



                #print $fh "$fields[0], $field2, $protein_list, $field
+3, $min, $scoring\n";
            
            }
        }    
    }
    
    else
    {
        print "not matched\n";
        $scoring = 0;
        print $fh "Undef, $fields[0] $field2, Unmatched proteins, $fie
+ld3, $min, $scoring\n";
        print "Undef, $fields[0] $field2, Unmatched proteins, $field3,
+ $min, $scoring\n";

    }
    }
    

}

close($fh);
[download]

This is the code I am using to extract the protein names from the PubMed abstracts. But many lines in of the file "finalidlist" that consists of PubMed IDs is skipped. Can anyone help me whats the problem?