dbolser-ebi

ensrw@mysql-eg-prod-2.ebi.ac.uk:4239 (triticum_aestivum_variation_31_84_2)
> SELECT * FROM variation_set_structure;
+---------------------+-------------------+
| variation_set_super | variation_set_sub |
+---------------------+-------------------+
|                  11 |                 1 |
|                  11 |                 2 |
|                  11 |                 3 |
|                  12 |                 4 |

dbolser-ebi

#!/usr/bin/env perl

use 5.14.0;
use warnings;

use autodie qw(:all);

use DBI;

my $dsn = 

dbolser-ebi

i=0
while read -r file; do
    if (( i++ >= 3 )); then
        wait $jobpid 
    fi
    
    base=${file/*rnaseq\//}

    echo $base

dbolser-ebi

#!/bin/env perl

use strict;
use warnings;

use Bio::EnsEMBL::Registry;

## Notes

## See this blog post (compile and make Tabix!):

dbolser-ebi

DROP PROCEDURE IF EXISTS test.QueryTablesByName;

DELIMITER //

CREATE DEFINER=`ensrw`@`%` PROCEDURE `QueryTablesByName`(
  tableName VARCHAR(255),
  query     TEXT
)
BEGIN

dbolser-ebi

DROP PROCEDURE IF EXISTS test.RunQueryByDatabaseQuery;

DELIMITER //

CREATE DEFINER=`ensrw`@`%` PROCEDURE `RunQueryByDatabaseQuery`(
  myQuery       TEXT,
  databaseQuery TEXT
)
BEGIN

dbolser-ebi

#!/usr/bin/env perl

use strict;
use warnings;

die "pass a fasta and a vcf\n"
  unless @ARGV == 2;

my $fsa = $ARGV[0];
my $vcf = $ARGV[1];

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

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

> 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)