Question

I am trying to create a program in Perl that will read through thousands of characters that and attempt to find a matching string of characters. I need to print out the string plus the next five letters. I also need to print out the location of where it was found, i.e. how many letters in. I am pretty new to Perl. I’m just learning it in class now.

Here is the code I have so far:

#!/usr/bin/perl

$sequence = 'abcd';
$fileName = 'file.txt';

#Opening file
unless (open(fileName, $fileName)) {
    print "Cannot open file.";
    exit;
}
@tempArr = <fileName>;    #Adding the lines to an array
close fileName;           #closing the file
$characters = join('', @tempArr);    #making it a clean string
$characters =~ s/\s//g;               #removing white lines
if (characters =~ m/$sequence/i) {

    #Print $sequence and next five characters
}
else {
    print "Does not contain the sequence.";
}

exit;

file.txt will look like:

aajbkjklasjlksjadlasjdaljasdlkajs
aabasdajlakjdlasdjkalsdkjalsdkjds
askdjakldamwnemwnamsndjawekljadsa
abcassdadadfaasabsadfabcdhereeakj

I need to print out the “abcdheree”

Answer 1

To print $sequence & the 5 characters after it, try using :

if ($characters =~ m/$sequence.{5}/i) {
    print "$&\n";

(You forgot the $ on characters)

NOTE

• . mean any character
• {5} is a quantifier
• when using open, use 3 arguments like : open my $fh, "<", "$file" or die $!; See http://perldoc.perl.org/perlopentut.html
• always put use strict; use warnings; at the top of your script
• don’t forget $ on variables (you miss many ones)
• use my for declaring variables
• maybe a better approach than making one big string: you can process the array line by line like : foreach my $line (@tempArr) { #process $line }
• you call the array @melTemp1 that is never declared

FINALLY

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

my $sequence = 'abcd';
my $fileName = 'file.txt';

#Opening file
open my $fh, "<", $fileName or die "Cannot open file. [$!]";

my @tempArr = <$fh>;                    #Putting the file handle into an array
close $fileName;                        #closing the file handle

my $characters = join('', @tempArr);    #making it a big string
$characters =~ s/\s//g;                 #removing white spaces & tabs

if ($characters =~ m/$sequence.{5}/i) {
    print "$&\n";
}
else {
    print "Does not contain the sequence.";
}