subroutine redefined 2

[ailse]

Hi all - I am having a pretty frustrating time with the following small perl program - every time i try to run it, I get the same error: "subroutine match_positions redefined at line 73"

#!/usr/bin/perl
# Make restriction map from user queries on names of restriction enzymes

use strict;
use warnings;
use dna;    

open(INFILE,"c:/perl/source/program/outfile.txt");

# Declare and initialize variables
my %rebase_hash = (  );
my @file_data = (  );
my $query = '';
my $dna = <INFILE>;
my $recognition_site = '';
my $regexp = '';
my @locations = (  );


# Get the REBASE data into a hash, from file &quot;bionet&quot;
%rebase_hash = parseREBASE('bionet');

# Prompt user for restriction enzyme names, create restriction map
do {
    print &quot;Search for what restriction site for (or quit)?: &quot;;
    
    $query = <STDIN>;

    chomp $query;

    # Exit if empty query
    if ($query =~ /^\s*$/ ) {

        exit;
    }

    # Perform the search in the DNA sequence
    if ( exists $rebase_hash{$query} ) {

        ($recognition_site, $regexp) = split ( &quot; &quot;, $rebase_hash{$query});

        # Create the restriction map
        @locations = match_positions($regexp, $dna);

        # Report the restriction map to the user
        if (@locations) {
            print &quot;Searching for $query $recognition_site $regexp\n&quot;;
            print &quot;A restriction site for $query at locations:\n&quot;;
            print join(&quot; &quot;, @locations), &quot;\n&quot;;
        } else {
            print &quot;A restriction site for $query is not in the DNA:\n&quot;;
        }
    }
    print &quot;\n&quot;;
} until ( $query =~ /quit/ );

exit;

################################################################################
#
# Subroutine
#
# Find locations of a match of a regular expression in a string
#
# 
# return an array of positions where the regular expression
#  appears in the string
#

sub match_positions {

    my($regexp, $sequence) = @_;

    use strict;

   
    #
    # Declare variables
    #

    my @positions = (  );

    #
    # Determine positions of regular expression matches
    #
    
    while ( $sequence =~ /$regexp/ig ) {

        push ( @positions, pos($sequence) - length($&) + 1);
    }

    return @positions;
}

any ideas why i keep getting this error?

thanks in advance

 

[rosenk]

Do you have a match_positions sub in the dna module you're using?

 

[ishnid]

That message is suggesting that the match_positions subroutine is being defined twice, though I don't see it in that code. What is 'dna' that you're importing? Is it possible that there's a sub called match_positions defined in that too?

Either way, if I were you, I'd change the name of your match_positions if it's not easy to find wherever else it's defined.

HTH

 

[ailse]

thanks both of you, that was exactly the problem! I was trying to keep all my subroutines separate in a different module, but i guess that one slipped through the net

 

[mikevh]

I don't think it has any bearing on the problem you mentioned, but I notice you've got a 'use strict' inside sub 'match_positions', in addition to the one at the top of the file. Is there a reason for the second 'use strict'? Seems unnecessary, as the scope of the first one includes the subroutine.