Trying to use substring to find a reverse complement in DNA,

tryingnottofailmytes has asked for the wisdom of the Perl Monks concerning the following question:

Hi. Obviously I'm new here. I'm a biology student playing in a CS class this semester and I have a final on Tuesday. Theres a lot of stuff I don't understand, so I'm hoping you guys can help me out. I'm trying to get the reverse complement of a string of DNA w/o using s// or tr/// and HAVE to use substring. Its a practice problem in our book that I'm working on. What I have so far

my $dna = 'atgAAAAAAAAAAGGGGGGGGGGTTTTTTTTCCCCCCCCCCCCagtcatc';
$dna = uc$dna;
print "$dna\n";
my $revDNA= reverse $dna;
print "$revDNA\n";
my $length = length$revDNA;
my $complement = '';
for (my $i=0;$i>$length-1; $i++)
{
    my $base= substr($revDNA,$i,1);
    if ($base eq 'A') { 
    $base = 'T'; 
    }
    elsif ($base eq 'T') { 
    $base = 'U'; 
    }
    elsif ($base eq 'G') { 
    $base = 'C'; 
    }
    elsif ($base eq 'C') { 
    $base = 'G'; 
    }
     $complement.=$base;
     
}
print $complement, "\n";
exit;
[download]

I don't really understand why this isn't working I'm not sure what the differences is between my and the posted solution, which has the for loop go backwards instead of forwards.... Can anyone offer any help?

Comment on Trying to use substring to find a reverse complement in DNA, Download Code

Replies are listed 'Best First'.
Re: Trying to use substring to find a reverse complement in DNA, by RichardK (Parson) on Dec 05, 2015 at 23:12 UTC
The condition on your for loop is the wrong way round, you need to use less than not greater than, here:- `$i>$length-1;` If you want to know how to fix these things for yourself try the basic debugging checklist	[reply] [d/l]
Re^2: Trying to use substring to find a reverse complement in DNA, by AnomalousMonk (Archbishop) on Dec 06, 2015 at 02:32 UTC
... you need to use less than not greater than ... I would say tryingnottofailmytes needs to use less-than-or-equal `$i <= $length-1` as the `for`-loop condition in the OPed code. Give a man a fish: `<%-{-{-{-<`	[reply] [d/l] [select]
Re^2: Trying to use substring to find a reverse complement in DNA, by tryingnottofailmytes (Novice) on Dec 05, 2015 at 23:24 UTC
THANK YOU SO MUCH!!!! This is my problem, I get really close in my code (at least I think I do) and I can't find the problems and I freak out and get a terrible score...	[reply]
Re: Trying to use substring to find a reverse complement in DNA, by johngg (Canon) on Dec 06, 2015 at 00:16 UTC
Rather than the series of `if { ... } elsif { ... } ...` tests you could use a hash table to look up the base and use it as the fourth argument to substr to replace the original. `$ perl -Mstrict -Mwarnings -E ' my $dna = q{AAGGTTCC}; my %compLU = ( A => q{T}, T => q{U}, G => q{C}, C => q{G}, ); my $complement = $dna; for my $idx ( 0 .. length( $complement ) - 1 ) { substr $complement, $idx, 1, $compLU{ substr $complement, $idx, 1 +}; } say $dna; say $complement;' AAGGTTCC TTCCUUGG $` [download] I hope this is of interest. Cheers, JohnGG	[reply] [d/l] [select]
Re: Trying to use substring to find a reverse complement in DNA, by Anonymous Monk on Dec 06, 2015 at 04:40 UTC
Just another way - using the transliteration operator. `my $dna = 'TAgc'; my $rc = uc reverse $dna =~ tr/ATGCatgc/TUCGtucg/r; print "$dna\n$rc";` [download] Prints `TAgc GCTU` [download]	[reply] [d/l] [select]
Re^2: Trying to use substring to find a reverse complement in DNA, by Cristoforo (Curate) on Dec 06, 2015 at 04:47 UTC
Could also say: `my $rc = reverse uc($dna) =~ tr/ATGC/TUCG/r;` [download] Laurent_R said Except that the OP said: without using s// or tr///. That's part of the assignment. Yes, my bad.	[reply] [d/l]
Re^2: Trying to use substring to find a reverse complement in DNA, by Laurent_R (Canon) on Dec 06, 2015 at 09:28 UTC
Yeah, it seems much simpler and I would probably go for something along these lines. Except that the OP said: without using s// or tr///. That's part of the assignment.	[reply]
Re: Trying to use substring to find a reverse complement in DNA, by BillKSmith (Monsignor) on Dec 06, 2015 at 14:55 UTC
UPDATE: Please disregard this suggestion. I did not notice the explicit reverse. Your book ran the loop backwards to reverse the string. You can run it forward, but you must reverse the concatenation: `$complement = $base . $complement;` [download] Bill	[reply] [d/l]


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