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

In reply to Uninitialized value in substr command by lmtaylor

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