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

dbolser-ebi

[dbolser@ebi-001 VCFLoad_simple]$ cat calculate_frequency.sql

-- 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

dbolser-ebi

{{Taxobox
| image = Candida albicans 2.jpg
| image_width = 250px
| regnum = [[Fungi]]
| division = [[Ascomycota]]
| divisio = [[Ascomycota]]
| classis = [[Saccharomycetes]]
| ordo = [[Saccharomycetales]]
| familia = [[Saccharomycetaceae]]
| genus = ''[[Candida (genus)|Candida]]''

dbolser-ebi

10495  git init
10496  git remote add origin git@github.com:dbolser-ebi/VCFLoad-simple.git
10497  git add load_vcf_simple.plx 
10498  git commit -m 'first commit'
10499  git push
10500  git rebase origin
10501  git rebase origin/master
10502  git rebase origin master
10503  git remote -v
10504  git fetch

dbolser-ebi

ensrw@mysql-eg-prod-1.ebi.ac.uk:4238 (solanum_lycopersicum_variation_27_80_250)
> SELECT COUNT(*), COUNT(DISTINCT allele_code_id), COUNT(DISTINCT allele) FROM allele_code; 
+----------+--------------------------------+------------------------+
| COUNT(*) | COUNT(DISTINCT allele_code_id) | COUNT(DISTINCT allele) |
+----------+--------------------------------+------------------------+
|  1136037 |                        1136037 |                      0 |
+----------+--------------------------------+------------------------+
1 row in set (2 min 11.99 sec)

dbolser-ebi

url=http://ves-ebi-60:8045/solr
core=transPlant-IPK

curl "${url}/${core}/update" \
    -H 'Content-type:application/xml' \
    -d '<delete><query>database_name:GEBIS</query></delete>'

dbolser-ebi

We have 2 'staging' databases that we use to prepare alternating
releases of our data. One staging machine is a copy of what's
currently 'live' and the other is the place where the next
release is prepared (pre-live if you like).

We have 3 'production' databases where DB heavy processes are run
in preparation for putting a database onto 'pre-live'.

We have 3 'development' databases where we run ad-hock analysis.

dbolser-ebi

> SELECT COUNT(DISTINCT species_set_id)
FROM plantsx INNER JOIN species_set USING (genome_db_id)
INNER JOIN method_link_species_set USING (species_set_id) WHERE method_link_id = 401
GROUP BY method_link_id;
+--------------------------------+
| COUNT(DISTINCT species_set_id) |
+--------------------------------+
|                             43 |
+--------------------------------+
1 row in set (0.01 sec)

dbolser-ebi

#!/usr/bin/env perl

use strict;
use warnings;

use Bio::EnsEMBL::Registry;

Bio::EnsEMBL::Registry->
  load_registry_from_db(
    -host => 'mysql-eg-prod-3.ebi.ac.uk',

dbolser-ebi

mysql-staging-2-ensrw hordeum_vulgare_core_30_83_2 -Ne '
  SELECT CONCAT(">", name, char(10), sequence)
  FROM temp_name INNER JOIN seq_region USING (name)
  INNER JOIN dna USING (seq_region_id)' \
      > Data/Hv_IBSC_PGSB_v2/bac_assemblies/morex.fasta