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Re: How can one get the correct results of all combinations with bigger input files?

by BrowserUk (Pope)
on Apr 27, 2013 at 06:19 UTC ( #1030928=note: print w/ replies, xml ) Need Help??


in reply to How can one get the correct results of all combinations with bigger input files?

suggest me necessary corrections in the script for getting all possible combinations.

You cannot.

Firstly, you cannot with the code you've posted because glob (including bsd_glob) produce all their results internally before handing them back and given the size of your input files, you will run out of memory -- no matter how much you have -- long before all the combinations have been generated.

But, even if you switched to using a proper iterating generator, that constructed your combinations one at a time, so avoiding memory exhaustion, with the size of your input files and the combinatorial explosion they represent, it would take years (if not decades) for your script to complete.

The bottom line is, you are going to have to learn that using brute force algorithms with genomic datasets is rarely feasible.

I request the perl monks to go through the script

Quite frankly, I think you are taking the piss. This place is not a code writing service.

Every time you post, you simply re-post the code given to you as a reply to your last question, and "request" other people to make changes that you are apparently too lazy to try and work out yourself. And you seem to have been pursuing this same strategy for all of the 2+ years you've been coming here.

I don't think this tactic will work for much longer.


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Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
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Comment on Re: How can one get the correct results of all combinations with bigger input files?
Re^2: How can one get the correct results of all combinations with bigger input files?
by supriyoch_2008 (Scribe) on Apr 29, 2013 at 05:27 UTC

    Hi BrowserUK,

    Thanks for your comments.

    With regards,

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