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Re: Reducing memory footprint when doing a lookup of millions of coordinates

by repellent (Priest)
on Mar 04, 2011 at 06:59 UTC ( [id://891374]=note: print w/replies, xml ) Need Help??

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  1. or download this
      chromosome = chr2
      starting   = 21000
      ending     = 23200
    
  2. or download this
    $ time perl -alne 'print join q{,} => @F[4,5,6,9] if $. > 3' hg19.fa.o
    +ut | psql -qc "
      CREATE TABLE tt (chromosome text, starting integer, ending integer, 
    +feature text);
    ...
     chr2       |    21258 |  21370 | MIRb
     chr2       |    22095 |  23394 | L1PA14
    (2 rows)
    

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