Uninitialized value in division and Illegal division by zero fix

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

I have the following code to get the nucleotide frequency of DNA subfragments.

my $file1=shift;
my @array=('A','T','C','G','AA','AT','AG','AC','TA','TT','TG','TC','GA
+','GT','GG','GC','CA','CT','CG','CC','AAA','AAT','AAG','AAC','ATA','A
+TT','ATG','ATC','AGA','AGT','AGG','AGC','ACA','ACT','ACG','ACC','TAA'
+,'TAT','TAG','TAC','TTA','TTT','TTG','TTC','TGA','TGT','TGG','TGC','T
+CA','TCT','TCG','TCC','GAA','GAT','GAG','GAC','GTA','GTT','GTG','GTC'
+,'GGA','GGT','GGG','GGC','GCA','GCT','GCG','GCC','CAA','CAT','CAG','C
+AC','CTA','CTT','CTG','CTC','CGA','CGT','CGG','CGC','CCA','CCT','CCG'
+,'CCC','AAAA','AAAT','AAAG','AAAC','AATA','AATT','AATG','AATC','AAGA'
+,'AAGT','AAGG','AAGC','AACA','AACT','AACG','AACC','ATAA','ATAT','ATAG
+','ATAC','ATTA','ATTT','ATTG','ATTC','ATGA','ATGT','ATGG','ATGC','ATC
+A','ATCT','ATCG','ATCC','AGAA','AGAT','AGAG','AGAC','AGTA','AGTT','AG
+TG','AGTC','AGGA','AGGT','AGGG','AGGC','AGCA','AGCT','AGCG','AGCC','A
+CAA','ACAT','ACAG','ACAC','ACTA','ACTT','ACTG','ACTC','ACGA','ACGT','
+ACGG','ACGC','ACCA','ACCT','ACCG','ACCC','TAAA','TAAT','TAAG','TAAC',
+'TATA','TATT','TATG','TATC','TAGA','TAGT','TAGG','TAGC','TACA','TACT'
+,'TACG','TACC','TTAA','TTAT','TTAG','TTAC','TTTA','TTTT','TTTG','TTTC
+','TTGA','TTGT','TTGG','TTGC','TTCA','TTCT','TTCG','TTCC','TGAA','TGA
+T','TGAG','TGAC','TGTA','TGTT','TGTG','TGTC','TGGA','TGGT','TGGG','TG
+GC','TGCA','TGCT','TGCG','TGCC','TCAA','TCAT','TCAG','TCAC','TCTA','T
+CTT','TCTG','TCTC','TCGA','TCGT','TCGG','TCGC','TCCA','TCCT','TCCG','
+TCCC','GAAA','GAAT','GAAG','GAAC','GATA','GATT','GATG','GATC','GAGA',
+'GAGT','GAGG','GAGC','GACA','GACT','GACG','GACC','GTAA','GTAT','GTAG'
+,'GTAC','GTTA','GTTT','GTTG','GTTC','GTGA','GTGT','GTGG','GTGC','GTCA
+','GTCT','GTCG','GTCC','GGAA','GGAT','GGAG','GGAC','GGTA','GGTT','GGT
+G','GGTC','GGGA','GGGT','GGGG','GGGC','GGCA','GGCT','GGCG','GGCC','GC
+AA','GCAT','GCAG','GCAC','GCTA','GCTT','GCTG','GCTC','GCGA','GCGT','G
+CGG','GCGC','GCCA','GCCT','GCCG','GCCC','CAAA','CAAT','CAAG','CAAC','
+CATA','CATT','CATG','CATC','CAGA','CAGT','CAGG','CAGC','CACA','CACT',
+'CACG','CACC','CTAA','CTAT','CTAG','CTAC','CTTA','CTTT','CTTG','CTTC'
+,'CTGA','CTGT','CTGG','CTGC','CTCA','CTCT','CTCG','CTCC','CGAA','CGAT
+','CGAG','CGAC','CGTA','CGTT','CGTG','CGTC','CGGA','CGGT','CGGG','CGG
+C','CGCA','CGCT','CGCG','CGCC','CCAA','CCAT','CCAG','CCAC','CCTA','CC
+TT','CCTG','CCTC','CCGA','CCGT','CCGG','CCGC','CCCA','CCCT','CCCG','C
+CCC');

my $name1="";
my $seq1="";
my %counts=();
my %counts_1=();
my %counts_2=();
my %counts_3=();
my %counts_4=();
my %total_mono=();

open (IN, "<$file1") or die ("Couldn't open file $file1\n");

while (my $i=<IN>){
  next unless ($i =~ /\w+/);
  chomp($i);
  if ($i =~ /^>(\S+)/){
    unless ($seq1 eq ""){
      $seq1 =~ s/[^ATCG]//g;
      &process_nuc($seq1, $name1);
    }
    $seq1="";
    $name1=$1;
  }else{
    $seq1.=uc($i);
  }
}
close IN;
$seq1 =~ s/[^ATCG]//g;
&process_nuc($seq1, $name1);


print "Matrix_";
print scalar(@array);
for (my $k=0; $k<@array; $k++){
  print "\t$array[$k]";
}print "\n";

my %norm_1=();
my %norm_2=();
my %norm_3=();
my %norm_4=();

foreach my $k (keys (%counts)){
  print "$k";

60  my $value=0;
61  $norm_1{'A'}=$counts_1{$k}{'A'}/$total_mono{$k};
62  $norm_1{'T'}=$counts_1{$k}{'T'}/$total_mono{$k};
63  $norm_1{'C'}=$counts_1{$k}{'C'}/$total_mono{$k};
64  $norm_1{'G'}=$counts_1{$k}{'G'}/$total_mono{$k};
[download]

When I executed, I got results and the following error message:

Use of uninitialized value in division (/) at ./n_f.pl line 61.

Illegal division by zero at ./n_f.pl line 61.

I tried to use eval BLOCK as recomended in http://www.perlmonks.org/?node_id=369002, but it didn´t help that much because I get the same error message. I know that first message is a warning, but how can I know if this affects my results?.

Also, I´m not quite sure if the second message is an error or a warning, so I don´t know if this made the script to stop.

I´ll appreciate the help.

Comment on Uninitialized value in division and Illegal division by zero fix Download Code

Replies are listed 'Best First'.
Re: Uninitialized value in division and Illegal division by zero fix by AppleFritter (Vicar) on Jul 09, 2014 at 17:47 UTC
Well, you never populate `%total_mono` in any way (in the code you posted). Therefore, `$total_mono{$k}` is undefined, no matter what `$k` contains. And an undefined value is interpreted as zero in a numeric context, and division by zero does not work, of course (see Meaning Of error in perl for a recent discussion). It's impossible to say how to proceed from here without knowing more about what you want to accomplish. Also, some general notes: Please, don't add linenumbers to your code like that; it just makes it syntactically invalid, and monks who want to help will have to remove them again. Please use comments instead. Even with the line numbers removed, your code doesn't compile due to a missing closing curly brace. Please post working code. Your code calls a subroutine, `process_nuc`, that is not included. Please post complete code. You read from `$file1`, but we don't know what that file might contain. Please share some sample data. Here are some more resources on how to ask questions effectively: On asking for help How do I post a question effectively? How do I compose an effective node title? I know what I mean. Why don't you? How (Not) To Ask A Question Clean your room XY Problem The SSCCE: Short, Self Contained, Correct (Compilable) Example Please help us help you. Thanks!	[reply]
Re: Uninitialized value in division and Illegal division by zero fix by Old_Gray_Bear (Bishop) on Jul 09, 2014 at 17:42 UTC
You are getting the error in line 61 because the denominator is zero, and division by zero is not defined (see the "Proof that 2 = 1" for example). The fix is to either: Check the denominator and skip the calculation if you are going to have a divide-by-zero. Debug the code and determine why `$total_mono{$k}` is not getting updated like you think it ought to be. ---- I Go Back to Sleep, Now. OGB	[reply] [d/l]
Re: Uninitialized value in division and Illegal division by zero fix by toolic (Bishop) on Jul 09, 2014 at 17:11 UTC
Tip #4 from the Basic debugging checklist ... Data::Dumper `use Data::Dumper; print Dumper(\%total_mono);` [download]	[reply] [d/l]
Re: Uninitialized value in division and Illegal division by zero fix by PerlSufi (Friar) on Jul 09, 2014 at 18:46 UTC
Listen to everything the other monks have previously told you as far as asking a question on here. It is not totally clear what the goal of your script is, either. You simply want to read a fasta file and calculate the percentage of occurances for each nucleotide? I have done this before, so I will try to help you. Also, It appears that you are trying to read a fasta file. Why are you shifting the file in the beginning? Please, do file handle like this instead: `my $file = '/path/to/file.txt'; open (my $fh, '<', $file) or die "Could not open file '$file' $!";` [download] Update: So, if you delete the subroutine reference `&process_nuc` from your first while loop, the code sucessfully reads a fasta file into `$seq1` After that, you're gonna need to loop through it and increment each time a nucleo tide is found, then do your division for percentage.	[reply] [d/l] [select]
Re: Uninitialized value in division and Illegal division by zero fix by AnomalousMonk (Archbishop) on Jul 09, 2014 at 22:48 UTC
It's not entirely clear to me what you're trying to do, but the `my @array=('A','T','C','G','AA','AT','AG', ..., 'CCCA','CCCT','CCCG','CCCC');` array and other code suggests you are iterating over every possible permutation of one through four of the `A T C G` bases and searching a string for and counting every occurrence of each of these substrings. If so, there's an easier, probably faster, way. The following code can probably use more error checking, but as I don't know just what you're doing, I'll leave that to you. I also do not claim it's the fastest possible approach. HTH. Read more... (4 kB)	[reply] [d/l] [select]
Re: Uninitialized value in division and Illegal division by zero fix by johngg (Canon) on Jul 10, 2014 at 09:16 UTC
Not addressing your problem but you might be able to save some typing and avoid mistakes by building your `@array` programmatically. The following code uses a recursive subroutine to construct an anonymous array (`$raTerms`), which is then dereferenced (`@$raTerms`) and printed. Running it with a maximum of three letters for brevity here. `use strict; use warnings; use 5.014; my $raItems = [ qw{ A T G C } ]; my $raTerms = []; makeCombos( $raTerms, 3, $raItems ); say for @$raTerms; sub makeCombos { my( $raTerms, $iters, $raItems, @terms ) = @_; my @localTerms; if ( @terms ) { push @localTerms, map { my $item = $_; map { $_ . $item } @terms } @$raItems; } else { push @localTerms, @$raItems; } $iters --; push @$raTerms, @localTerms; return $iters ? makeCombos( $raTerms, $iters, $raItems, @localTerms ) : (); }` [download] The output. Read more... (515 Bytes) I hope this is helpful. Cheers, JohnGG	[reply] [d/l] [select]
Re: Uninitialized value in division and Illegal division by zero fix by redbull2012 (Sexton) on Jul 10, 2014 at 09:41 UTC
Hmmm, First: `#... if ($i =~ /^>(\S+)/){ # Captured in $1 unless ($seq1 eq ""){ $seq1 =~ s/[^ATCG]//g; #if match The s/// clears $1 &process_nuc($seq1, $name1); } $seq1=""; $name1=$1; #hence $name1 may be undef #...` [download] Second: Why do you print out all elements in "@array"? Ok, this may be test code. Third: Why do you create %norm_2, %norm_3, %norm_4 (more...) without using them ??? Fourth: Where do you get the data for %counts_1, %total_mono ??? Fifth: What does process_nuc() do???? .... ..	[reply] [d/l]