dbolser-ebi

#! perl

use strict;
use warnings;

use Bio::EnsEMBL::Registry;

my $species = 'sorghum_bicolor';

warn "Loading registry\n";

dbolser-ebi

##gff-version   3
##sequence-region   1812.scaffold02418 1 1541
1812.scaffold02418      AUGUSTUS        gene    1       1541    0.29    -       .       ID=Bv_56410_edoq;Name=Bv_56410_edoq
1812.scaffold02418      AUGUSTUS        mRNA    1       1541    0.29    -       .       ID=Bv_56410_edoq.t1;Parent=Bv_56410_edoq;Name=Bv_56410_edoq.t1 88.9%;Note=cDNAcoverage_88.9%
1812.scaffold02418      AUGUSTUS        intron  1       218     0.39    -       .       ID=Bv_56410_edoq.t1.intron;Parent=Bv_56410_edoq.t1
1812.scaffold02418      AUGUSTUS        CDS     219     293     0.67    -       0       ID=Bv_56410_edoq.t1.CDS;Parent=Bv_56410_edoq.t1
1812.scaffold02418      AUGUSTUS        intron  294     610     0.83    -       .       ID=Bv_56410_edoq.t1.intron;Parent=Bv_56410_edoq.t1
1812.scaffold02418      AUGUSTUS        CDS     611     655     0.83    -       0       ID=Bv_56410_edoq.t1.CDS;Parent=Bv_56410_edoq.t1
1812.scaffold02418      AUGUSTUS        start_codon     653     655     .       -       0       ID=Bv_564

dbolser-ebi

#!perl

use strict;
use warnings;

## Easy manipulation of sets of integers (arbitrary intervals)
use Set::IntRange;


## Files

dbolser-ebi

jis

dbolser-ebi

22:24 < dbolser> hello, I'm calling 'the same' script in two different 
                 contexts, on one it works, on one it doesn't:
22:24 < dbolser> http://www.ebi.ac.uk/~dbolser/Genoverse/?r=3:9874770-9902882
22:24 < dbolser> http://dev.transplantdb.eu/node/4328

22:27 < yansanmo> dbolser, you don't have jquery-ui on the second ?
22:27 < yansanmo> and jquery-ui contains .sortable() function

22:27 < dbolser> yansanmo: that's weird, I should have! Thanks for this 
                 information!

dbolser-ebi

DROP   TABLE IF EXISTS temp_individual_genotype_a;
Query OK, 0 rows affected (0.02 sec)

CREATE TABLE           temp_individual_genotype_a
    -> (INDEX pk_ish (variation_id, population_id, allele_code_id))
    -> SELECT
    ->   variation_id, population_id, allele_code_id_1 AS allele_code_id,
    ->   `COUNT(*)` AS N
    -> FROM temp_individual_genotype_a1 LIMIT 6000000;
Query OK, 6000000 rows affected, 1 warning (6.08 sec)

dbolser-ebi

-- Try adding an index...
#ALTER TABLE tmp_individual_genotype_single_bp
#  ADD INDEX allele_1_idx (allele_1),
#  ADD INDEX allele_2_idx (allele_2);

# Query OK, 277545309 rows affected (43 min 29.78 sec)

-- The above index seems to have no impact on query execution time
-- below, as the individual_id_idx is picked instead of either of

dbolser-ebi

dbolser@dbolser-laptop ~ $ time curl  http://$mydomain:9213
{
  "status" : 200,
  "name" : "urgi_node3",
  "cluster_name" : "urgi_tribe_demo",
  "version" : {
    "number" : "1.4.3",
    "build_hash" : "36a29a7144cfde87a960ba039091d40856fcb9af",
    "build_timestamp" : "2015-02-11T14:23:15Z",
    "build_snapshot" : false,

dbolser-ebi

1424361431: Done 116000
1424361431: Done 117000
1424361431: Done 118000
1424361431: Done 119000
1424361431: Done 120000
1424361431: Done 121000
1424361431: Done 122000
1424361431: Done 123000
1424361431: Done 124000
1424361431: Done 125000

dbolser-ebi

Total Elapsed Time = 8.131346 Seconds
  User+System Time = 7.401346 Seconds
Exclusive Times
%Time ExclSec CumulS #Calls sec/call Csec/c  Name
 49.8   3.689  3.689 114036   0.0000 0.0000  Bit::Vector::Resize
 11.8   0.880  0.905 236667   0.0000 0.0000  Set::IntRange::Interval_Fill
 8.34   0.617  0.745 221030   0.0000 0.0000  Set::IntRange::Max
 5.51   0.408  4.097 114036   0.0000 0.0000  Set::IntRange::Resize
 3.13   0.232  0.232  31690   0.0000 0.0000  Bit::Vector::Norm
 1.82   0.135  0.197  31690   0.0000 0.0000  Set::IntRange::new