"e.coli.replaced becomes e.coli (which is fine)

It doesn't. With your code it becomes "e.coli.".

"but z.mays becomes z.may (which isn't)."

Don't assume what rindex returns, try this for your test case:

print rindex( $name, q{replaced} );

[download]

A simpler way of doing this would be:

my $name = "e.coli.replaced";
$name =~ s/.replaced//;

[download]

Should you actually wish the outcome to be as you specified and not what your code actually does.

Update: Fixed typo

Update 2: Dang, this is a must read, catches my mistake.

In reply to Re: Problem with substr by marto
in thread Problem with substr by newbie1991

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