Hello,
It has been a while, so I hope you all have a little patience.

I have written a short script to do a little text mining. I have one file that contains a list of words/terms (new line separated), and a second file that contains a fairly substantial amount of text. I then want to take each term from the first file in turn and count the number of occurances of that term in the second file.

The output would be something like:

Term         Number
----------------------
term1          10
term2           1
my term3       16

[download]

I am not bothered about the output as yet. The problem I do have, however, is that I am using a regular expression that does not seem to work for a term that consists of multiple words, i.e. 

term1
term2
my term 3

[download]

The code I have at the moment is: 

#!/usr/bin/perl -w

use warnings;
use strict;
use Getopt::Long;

my $terms = "";
my $pathway_abstracts = "";
my %word_counts;
my $count = 0;
my %term_score;
my $term_frequency_score = 0;
my $word_number = 0;


##################### GET USER INPUT #################################
+##########

GetOptions( "pathway_abstracts=s" => \$pathway_abstracts,
            "terms_file=s" => \$terms
          );


################### STORE IN ARRAYS ##################################
+##########
# store pathway abstract in arrays
open(IN, "$pathway_abstracts" ) || die "$!";
my @array_1 = <IN>;
close(IN);

# store terms in array
open(IN2, "$terms" ) || die "$!";
my @array_2 = <IN2>;
close(IN2);


#################### CREATE HASHES OF TERMS ##########################
+##########
foreach my $key (@array_2)    # assign a score of 0 to each term
{
  chomp($key);
  $term_score{$key} = 0;
}


######################################################################
+##########

print("Term\t| ");
print("Number\t| ");
print("Frequency\n");
print("----------------------------------------------------\n");


for (my $j = 0; $j < @array_2; $j++)        # loop through each search
+ term
{
  chomp($array_2[$j]);
  my $phenotype_term = $array_2[$j];         # set the search term

  for(my $i = 0; $i < @array_1; $i++)        # loop through each line 
+in the document
  {
    my @word_array = split(/\s/, $array_1[$i]);         # split abstra
+cts on each word
    $word_number = $word_number + scalar(@word_array);      # find out
+ how many words are in abstracts

    foreach my $word (@word_array)          # look through each word i
+n current line
    {
      if($word =~ /\b\Q$phenotype_term\E\b/)   #  does line contain fi
+lter term
      {
        $term_score{$array_2[$j]} = $term_score{$array_2[$j]} + 1;    
+# increment term count
      }
    }
  }
  $term_frequency_score = $term_score{$array_2[$j]} / $word_number;   
+# calculate term frequency
  
  print($array_2[$j]."\t  ");                     # print the term
  print($term_score{$array_2[$j]}."\t  ");        # print the number o
+f term occurances
  print($term_frequency_score."\n");              # print the frequenc
+y
}

[download]

Could anyone please let me know why the \b or \B do not appear to work here in the regualr expression:
$word =~ /\b\Q$phenotype_term\E\b/

Any help is very much appreciated.
many thanks,
MonkPaul.

In reply to Regex word boundries by MonkPaul

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