Re: Memory Usage in Regex On Large Sequence

in reply to Memory Usage in Regex On Large Sequence

Questions:

How many threads are you creating?
what sorts of strings does $motif contain? Is it anything other than A/C/G/T x N ? If so, what? Otherwise, what's the maximum length of $motif?

Dave.

Comment on Re: Memory Usage in Regex On Large Sequence

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Re^2: Memory Usage in Regex On Large Sequence by bernanke01 (Beadle) on Sep 25, 2006 at 18:02 UTC
Hi, It's 10 threads, but repeats at 3 as well. For now, the motifs are just 6 strings of GCAT of 5 or 6 letters each. In theory I'd like to use more complex motifs of course. So, here are my current motif-list: `GCGTG GTGCG CACGC CGCAC CACGTG GTGCAC` [download]	[reply] [d/l]
Re^3: Memory Usage in Regex On Large Sequence by dave_the_m (Monsignor) on Sep 25, 2006 at 19:38 UTC
In that case, I can't see any good reason why replacing `index(..,"GTGCAC",...)` with `/GTGCAC/` should use any more memory, except that if `$sequence` is very large, and if somewhere in the program (eg from an included module), $`, $& or $' is used, then perl has to take a complete copy of `$sequence` each time, which might put you about the threshold. Dave.	[reply] [d/l] [select]
Re^4: Memory Usage in Regex On Large Sequence by bernanke01 (Beadle) on Sep 25, 2006 at 20:16 UTC
Ahh, interesting -- is there a way to verify if that is happening, or to prevent the copying from going on?	[reply]
Re^5: Memory Usage in Regex On Large Sequence by BrowserUk (Patriarch) on Sep 26, 2006 at 00:19 UTC
Re^6: Memory Usage in Regex On Large Sequence by bernanke01 (Beadle) on Sep 26, 2006 at 22:41 UTC
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