|laziness, impatience, and hubris|
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:
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