Hi guys. I am totally new to perl. Just started to work on it a week ago..please excuse my stupidity in btwn...Glad to be a part of this monastery..I'm trying to build a simple RegEX text parser. I will be having a three input files . first one is GENE which contains a list of gene names second one TARGET contains a list of protein locations inside the cell. third one IF is my input full text which i have made it into a single line one. Now while parsing I will be looking for the GENE entry, verb, and TARGET entry. in a single line of the text. if three are present then I print them out.

 #! usr/bin/perl
use strict;
use warnings;

# opening the input lexicons

open (GENE,"/home/stanley/Desktop/Gene.txt");
open (TARGET, "/home/stanley/Desktop/Target.txt");

my $target;
my $gene;

# opening fulltext

open (IF, "/home/stanley/Desktop/18048320.txt");
my $text = <IF>;
my @splittext = split (/[.] [A-Z]/, $text);
close (IF);

# opening output file

open (OF, ">/home/stanley/Desktop/Local.txt");

# Parsing Text

for $gene (<GENE>) {

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

            foreach my $line (@splittext) {
                if ($line =~ /.+?($gene).*(localizes to|held|located i
+n|localization|translocated to|targets|reaches|exported|export).*($ta
+rget).+?/ig) {
                print OF $1."\t".$2."\t".$3."\n";
                }
            }
    
    }
} 
close (OF);
close (GENE);
close (TARGET);
[download]

____DATA___

gene.txt

pfrom1
pfama1
ama1
ha-pfrom1

target.txt

apicoplast
mitochondrion
rhoptry
rhoptries
golgi
dense granules
parasitophorous vacuole
micronemes
food vacuole
secretory vesicle
host cell

input txt
ompartmentalization of proteins into subcellular organelles in eukaryo
+tic cells is a fundamental mechanism of regulating complex cellular f
+unctions. Many proteins of Plasmodium falciparum merozoites involved 
+in invasion are compartmentalized into apical organelles. We have ide
+ntified a new merozoite organelle that contains P. falciparum rhomboi
+d-1 (PfROM1), a protease that cleaves the transmembrane regions of pr
+oteins involved in invasion. By immunoconfocal microscopy, PfROM1 was
+ localized to a single, thread-like structure on one side of the mero
+zoites that appears to be in close proximity to the subpellicular mic
+rotubules. Using antibodies to the merozoite surface protein-1 (MSP1)
+, a protein that is located in the merozoite plasma membrane (Fig. 3A
+), we demonstrated that HA-PfROM1 staining is intracellular, not colo
+calizing with the plasma membrane. In merozoites, PfAMA1 is located i
+n micronemes and thus separated from PfROM1. Toxoplasma gondii ROM1, 
+the orthologue of PfROM1, is located in the Golgi, secretory vesicles
+, and in micronemes (10; L. D. Sibley, unpublished data). For example
+, Plasmodium falciparum apical membrane antigen 1 (AMA1) is held in t
+he micronemes in merozoites inside of erythrocytes. For example, Plas
+modium falciparum apical membrane antigen 1 (AMA1) is held in the mic
+ronemes in merozoites inside of erythrocytes.
[download]

This a just a small part of the input file. Now what happens is that the parser checks for only the first GENE entry and then quits the loop. what I want is foreach of the geneentry it should take up all the target possibilities one by one and check for the pattern in each line of the text