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]