Well, some detail on what went wrong would help....

When I tried it against the sample data in your original post, I noticed two things:

1. You're testing for gi| at the beginning of the line, but your @array1 values start with >gi|. I had to remove the >; you'll have to either fix the $key = line to match your data, or fix the data to match your test...
2. You're populating a single element in array2. If you want each number to be an element of the array, you need to use qw(...), not qq(...).

If these are both copy-and-paste artifacts, pleave provide more detail on what the error is.

Sorry,

I should have been more specific.

The two problems that you noticed are not problems in my program, just in the example I gave in my question.

With the code that you posted I don't get any error - but I don't get any output either ;-( The $key is definately picking up values (e.g. gi|14028145 |) so I think the problem is with substr. Also, the values of @array2 are present in @array1 as I have checked.

Hope you can help.

Thanks!

Yes, but are you loading @array2 with qq or qw? You must use qw if your code is anything like the above.

Try this: add the line print "There are ", scalar(@array2), " elements\n";right after you assign to it, and see if it has as many elements as you think it does.

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