|Pathologically Eclectic Rubbish Lister|
Re: Searching array against hashby BrowserUk (Pope)
|on Aug 21, 2013 at 21:37 UTC||Need Help??|
I feel that there should be a more efficient way
There is. Your current process is ~O(900,000*60,000) = 54 billion.
If you reverse the logic of your lookups, by reading the list file into a hash first; you can then read the fasta file line by line and lookup the headers in the hash, which results in an O( 900,000 ) process.
Try this (untested) version which should run close to 60,000 times faster:
With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.