in reply to 2d Array - making an array for the column then adding the values

You say your problem is with extracting a column and summing it. That only takes one line (three without a module), so why did you present so much code? 

use List::Util qw( sum );

my $sum = sum map { $array[$_][$col] } 0..$#array;

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my $sum = 0;
for my $row (0..$#array) {
   $sum += $array[$row][$col];
}

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Please locate your problem, then come back if you can't fix it once you locate it.

By the way, 

      my $nextline = <FASTA>;
      if($nextline =~ /^(\S+)$/) {
        my $nextline = <FASTA>;
        if($nextline =~ /^\+(.*)\s/) {
          my $nextline = <FASTA>;
          if($nextline =~ /^(\S+)$/) {
            $qual = $1;

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causes lines to be skipped if an "if" is ever false. You want redo. And the unused captures needlessly slow down your matches. 
      my $nextline = <FASTA>;
      redo if $nextline !~ /^\S+$/;

      $nextline = <FASTA>;
      redo if $nextline !~ /^\+/;

      $nextline = <FASTA>;
      redo if $nextline !~ /^\S+$/;

      chomp( my $qual = $nextline );

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Re^2: 2d Array - making an array for the column then adding the values
by hansoffate (Novice) on Sep 21, 2009 at 02:30 UTC
    Thanks for your help. My PI doesn't want me to use any other modules other then the default ones that come installed with perl, so I can't use List::Util. I already have the the column assigned to a 1D array on line 121, but I believe it is all referenced. If I try to use this sub with a passed in @col, the total is calculated incorrectly. 

    sub score_count {
    my @arr = shift;
    my $total = 0;
    foreach my $score (@arr) {
      print "@$score ";       ##prints actual values; If @ taken out, 
+values printed are like ARRAY(0x95533e0)
    $total += @$score;    ##if @ is taken out the summation is somewhe
+re ~140915576; however, with the @, the values are still incorrect. 
    }
    print "$total\n";
    return $total;
}

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    Are you suggesting to not even use the column slice so it's a 1D array?

    Thanks for letting me know about if construct issue but I do want to skip the line if it is false so that code should be correct.

    Thanks for the help

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[d/l]

      List::Util does come with Perl.

      Thanks for isolating the problem. I was explaining it here while you were writing your post.

      The only thing I didn't cover is that references evaluate to the address of the referenced item when they are treated as a number.

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      My PI doesn't want me to use any other modules other then the default ones that come installed with perl, so I can't use List::Util.
      Firstly, List::Util is a core module, which means that it is one of "the default ones that come installed with perl". Feel free to use it, just as you are using Getopt::Std. Update: I didn't see ikegami's comment relating to this.

      Secondly, even if it were not a core module, you could reuse some of the module's source code. So, tell your PI (whatever that is) to put that in his pipe and smoke it!

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