Re: retrieving in the correct order

I take it the first array is relatively small? If so, you can just turn your loops inside out:

for my $i (@array2) {
    for my $line (@array1) {
        my $key = "gi|$i|";
        if (substr($line, 0, length $key) eq $key) {
            print $line;
        }
    }
}
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Notice how you don't even need a regex, just a simple string compare.

If array1 is sorted, you can speed this up a little by remembering where you left off.

Do not rebuke them with harsh words ... but rather lead them gently - with URLs - so that they may learn wisdom.

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Re^2: retrieving in the correct order by Anonymous Monk on Dec 16, 2004 at 20:21 UTC
Hi VSarkiss, Thanks for your solution but I can't get it to work! Maybe it's becuase my first array is quite big (~1000 sequences). But wouldn't this just slow it down? Thanks	[reply]
Re^3: retrieving in the correct order by VSarkiss (Monsignor) on Dec 16, 2004 at 20:47 UTC
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: 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... 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. Do not rebuke them with harsh words ... but rather lead them gently - with URLs - so that they may learn wisdom.	[reply] [d/l] [select]
Re^4: retrieving in the correct order by Anonymous Monk on Dec 16, 2004 at 21:24 UTC
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!	[reply]
Re^5: retrieving in the correct order by VSarkiss (Monsignor) on Dec 16, 2004 at 21:39 UTC
Re^6: retrieving in the correct order by Anonymous Monk on Dec 16, 2004 at 21:50 UTC
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Re^3: retrieving in the correct order by insaniac (Friar) on Dec 16, 2004 at 21:51 UTC
hey, check my code below, i tested it with a file with 3000 lines in it. `time cat gen.txt \| perl -w gen.pl` says: `real 0m0.139s user 0m0.109s sys 0m0.000s` [download] if you're still looking for an answer... -- to ask a question is a moment of shame to remain ignorant is a lifelong shame	[reply] [d/l] [select]