Uninitialized value in substr command

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

Hello. I'm trying to take a very large array and re-format it. The initial array looks something like this:

>123

ABD

CEF

GHI

>456

JKL

MNO

>789

That's obviously simplified, but that's the idea. I want to join the elements between the two lines that begin with '>' and then get rid of the lines that begin with the '>', so my final array looks something like this:

ABDCEFGHI

JKLMNO

Here is the code I've written to do it. My problem is, every time I run it, I get a million errors that all say "Use of uninitialized value in substr at line 19." But I can't figure out what value it's talking about.

 

#!/usr/bin/perl -w

my @contigfile = (">37","ABC","DEF","GHI","JKL","MNO","PQR","STU","VWX
+","YZ",">38");

my $element1 = 0;

my $element2 = 0;

# print @contigfile;

# print substr($contigfile[$element1],0,1);

# print $contigfile[$element1];

while ($contigfile[$element1]){

    if (substr($contigfile[$element1], 0, 1) eq '>'){

        do {

            ++$element2;

        } until (substr($contigfile[$element2], 0, 1) eq '>');

        $new = join('',@contigfile[($element1 + 1)..($element2 - 1)]);
 
        splice @contigfile, $element1, $element2, "$new";

        ++$element1;

        $element2 = $element1;

    }

}

print @contigfile;



exit;
[download]

I wrote this code to test my method before implementing it in my real program, which will take the array in from an input file. Only I can't figure out what this error is talking about. The commented out print commands work just fine. Does anyone see something that I'm missing?

Thank you so much for your help!

- Lisa

Comment on Uninitialized value in substr command Download Code

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Re: Uninitialized value in substr command by hippo (Archbishop) on Aug 20, 2014 at 21:28 UTC
`$element2` at least is running away and therefore you are trying to read beyond the end of `@contigfile` in your substr call. Hence the warning message. If you must do it using this algorithm (and TIMTOWTDI but it wouldn't have been my choice) it would be wise to test that both $element1 and $element2 are not outside the bounds of the array. I'd also suggest you use strict.	[reply] [d/l] [select]
Re^2: Uninitialized value in substr command by lmtaylor (Novice) on Aug 21, 2014 at 17:42 UTC
Thank you for your help! What does TIMTOWTDI mean?	[reply]
Re^3: Uninitialized value in substr command by Laurent_R (Canon) on Aug 21, 2014 at 18:01 UTC
TIMTOWTDI is one of the Perl mottoes: "there is more than one way to do it."	[reply]
Re: Uninitialized value in substr command by Laurent_R (Canon) on Aug 20, 2014 at 21:27 UTC
Well, if the array already exists, maybe try this (untested): `my $string = ""; my @new_array; for my $item (@contigfile) { if ( $item =~ /^>\d) { push @new_array, $string unless $string eq ""; $string = ""; } else { $string .= $item; } } push @new_array, $string; # takes care of the last element` [download] If you have a file, you should probably avoid using a temporary array (at least if you file is big), but rather do essentially the same thing directly in a `while` loop reading the file: `my $string = ""; while (my $line = <$input_fh>) { chomp $line; if ( $line =~ /^>\d) { push @new_array, $string unless $string eq "";; $string = ""; } else { $string .= $line; } } push @new_array, $string; # take care of the last element` [download] Update: fixed the typo indicated by Lotus1 (in the post just below) in the regex (I had inadvertently forgotten the '>'). Thanks to Lotus1.	[reply] [d/l] [select]
Re^2: Uninitialized value in substr command by Lotus1 (Vicar) on Aug 21, 2014 at 14:06 UTC
Laurent_R: I tested your code and got it working after fixing a typo in your regex. `if ( $item =~ /^>\d/ ) {`	[reply] [d/l]
Re^2: Uninitialized value in substr command by lmtaylor (Novice) on Aug 21, 2014 at 17:44 UTC
Thanks! I had to look up a few bits of your code to see what they meant, but now that I have I see that's a smart way to do it.	[reply]
Re: Uninitialized value in substr command by Anonymous Monk on Aug 20, 2014 at 21:53 UTC
Here is the code I've written to do it. My problem is, every time I run it, I get a million errors that all say "Use of uninitialized value in substr at line 19." But I can't figure out what value it's talking about. Why, it's obvious. `do { ++$element2; } until (substr($contigfile[$element2], 0, 1) eq '>');` [download] If `$configfile[$element2]` yields `undef`, the loop will never stop. Because `substr( undef, 0, 1 ) eq '>'` is never true. `perl -we 'do { print "hello\n" } until substr( undef, 0, 1 ) eq ">"' hello Use of uninitialized value in substr at -e line 1. hello Use of uninitialized value in substr at -e line 1. hello Use of uninitialized value in substr at -e line 1. hello Use of uninitialized value in substr at -e line 1. hello ...` [download]	[reply] [d/l] [select]
Re: Uninitialized value in substr command by Anonymous Monk on Aug 20, 2014 at 23:04 UTC
"Use of uninitialized value in substr at line 19." But I can't figure out what value it's talking about. Try adding `use diagnostics;` at the top of your program, you'll get a slightly longer explanation of errors and warnings. In this case the "uninitialized" warning means that one of the variables used had a value of `undef`, which happens e.g. when the variable has never been assigned anything, when you try to access array elements that you don't exist, or when the variable has been explicitly assigned `undef` at some point (see Declarations and undef). Also, another tool from the Basic debugging checklist is Data::Dumper, which makes it much easier to see your data structures (including `undef`). In this case you could have written `print Dumper(\@contigfile,$element1,$element2);` to see the current values of those variables.	[reply] [d/l] [select]
Re: Uninitialized value in substr command by choroba (Cardinal) on Aug 21, 2014 at 07:48 UTC
In your script, the `>456` header is missing before the second sequence. Here's how I would solve your task without BioPerl: `#!/usr/bin/perl use warnings; use strict; my @contigfile = qw( >37 ABC DEF GHI >456 JKL MNO PQR STU VWX YZ >38 ) +; my @result; for my $i (0 .. $#contigfile) { my $current = $contigfile[$i]; push @result, q() and next if 0 == index $current, '>'; $result[-1] .= $current; } print "$_\n" for @result;` [download] لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ	[reply] [d/l] [select]