#! usr/bin/perl
use strict;
use warnings;
use Lingua::EN::Sentence qw( get_sentences add_acronyms );

# opening the input lexicons
open (GENE,"Gene.txt") || die "Cannot open Gene.txt !!";
open (TARGET, "Target.txt") || die " Cannot open Target.txt !!";

my $target;
my $gene;

# opening fulltext and sentence breaking
open (IF, "Input.txt") || die " Cannot open Fulltext !!";
my $text = <IF>;
my $sentences=get_sentences($text);

close (IF);    
        

# opening output file

open (OF, ">results.txt");

# Parsing Text
my $verbs = "localized|held|located in|localization|translocated to|targets|reaches|exported|export";
while ($gene = <GENE>) {

chomp $gene;
	seek (TARGET,0,0);
	while ($target = <TARGET>) {
	chomp $target;

			foreach my $sentence (@$sentences) {
				if ($sentence =~ /($gene).+($verbs).+($target)/ig) {
				print OF $1."\t".$2."\t".$3."\t\t".$sentence."\n";
				}
			}
	
	}
} 
close (OF);
close (GENE);
close (TARGET);

##</code><code>##


_______MY RESULTS____

AMA1	held	micronemes		For example, Plasmodium falciparum apical membrane antigen 1 (AMA1) is held in the micronemes in merozoites inside of erythrocytes.
AMA1	located in	micronemes		In merozoites, PfAMA1 is located in micronemes and thus separated from PfROM1.
AMA1	translocated to	subpellicular microtubules		The protein AMA1 is then translocated to the food vacuole, apicoplast, subpellicular microtubules.
PfROM1	located in	micronemes		Toxoplasma gondii ROM1, the orthologue of PfROM1, is located in the secretory vesicles, Golgi, and in micronemes (10; L. D. Sibley, unpublished data).
PfROM1	located in	micronemes		PfROM1 was also thought to be located in micronemes (13), based on data localizing a PfROM1 construct that was missing two 5&#8242; exons which encode one of the transmembrane domains of PfROM1 (SI Figs.
AMA1	held	micronemes		For example, Plasmodium falciparum apical membrane antigen 1 (AMA1) is held in the micronemes in merozoites inside of erythrocytes.
AMA1	located in	micronemes		In merozoites, PfAMA1 is located in micronemes and thus separated from PfROM1.
AMA1	translocated to	subpellicular microtubules		The protein AMA1 is then translocated to the food vacuole, apicoplast, subpellicular microtubules.
PfROM1	located in	micronemes		Toxoplasma gondii ROM1, the orthologue of PfROM1, is located in the secretory vesicles, Golgi, and in micronemes (10; L. D. Sibley, unpublished data).
PfROM1	located in	micronemes		PfROM1 was also thought to be located in micronemes (13), based on data localizing a PfROM1 construct that was missing two 5&#8242; exons which encode one of the transmembrane domains of PfROM1 (SI Figs.