This isn't built around PDL, but I'd be surprised if there's not a simple way to adapt it to work with your PDL objects.


use strict;
use warnings;

my $target = "ATTCCGGG";

my @tests = qw/ ATTGCGGG ATACCGGC /;



foreach my $test ( @tests ) {

    print "Testing: Target: $target\tTest: $test\n";

    my @results = map {
        my ( $target_c, $test_c ) = (
            substr( $target, $_, 1 ),
            substr(   $test, $_, 1 )
        );
        ( $target_c ne $test_c ) ? [ $_, $target_c, $test_c ] : ();
    } 0 .. length( $target ) - 1;

    print "\t$_->[0]: $_->[1] -> $_->[2]\n" for @results;

}

[download]

Output:

Testing: Target: ATTCCGGG       Test: ATTGCGGG
        3: C -> G
Testing: Target: ATTCCGGG       Test: ATACCGGC
        2: T -> A
        7: G -> C

[download]

Dave

In reply to Re: mismatching characters in dna sequence by davido
in thread mismatching characters in dna sequence by prbndr

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