dbolser

#!perl

use strict;
use warnings;

=pod

Script to grab the peptide sequence of a given ID from the DB

=cut

dbolser

#!/usr/bin/env perl

$| = 1;

use strict;
use warnings;
use autodie;
use feature 'say';
use Class::Load 'load_class';
use Cwd 'cwd';

dbolser

Here is the error I'm seeing:

dmb@percy:AMDAPP$ bfgminer -n 
 [2013-07-24 11:57:07] Error -1001: clGetPlatformsIDs failed (no OpenCL SDK installed?)                    
 [2013-07-24 11:57:07] clDevicesNum returned error, no GPUs usable                    
 [2013-07-24 11:57:07] 0 GPU devices max detected                    

dmb@percy:AMDAPP$ bfgminer --version
bfgminer 3.1.3

dbolser

#!/usr/bin/perl

use Tie::File;
if(-e "AMDAPPlog.txt") {
        unlink("AMDAPPlog.txt"); 
}
$pkg_name="AMD-APP-SDK-v2.8.1.0-RC";
$version_appsdk="v2.8.1.0";
open(OUTPUT_LOG,'>', "AMD_APPSDK_v2.8.1.0.log");
my $steps =1;

dbolser

Example input...

# 
# More information on reference human assembly build 36:
# http://www.ncbi.nlm.nih.gov/projects/mapview/map_search.cgi?taxid=9606&build=36
#
# rsid  chromosome      position        genotype
rs4477212       1       72017   AA
rs3094315       1       742429  AA
rs3131972       1       742584  GG

dbolser

#!/usr/bin/env perl

# Projects generic features ... hopefully

use strict;
use warnings;

use Data::Dumper;

use Bio::EnsEMBL::Registry;

dbolser

> EXPLAIN SELECT COUNT(DISTINCT feature_stable_id), COUNT(DISTINCT feature_stable_id, somatic) FROM transcript_variation ; 
+----+-------------+----------------------+-------+---------------+---------------------+---------+------+----------+-------------+
| id | select_type | table                | type  | possible_keys | key                 | key_len | ref  | rows     | Extra       |
+----+-------------+----------------------+-------+---------------+---------------------+---------+------+----------+-------------+
|  1 | SIMPLE      | transcript_variation | index | NULL          | somatic_feature_idx | 132     | NULL | 64279473 | Using index |
+----+-------------+----------------------+-------+---------------+---------------------+---------+------+----------+-------------+


> EXPLAIN SELECT COUNT(DISTINCT feature_stable_id), COUNT(DISTINCT feature_stable_id, somatic) FROM transcript_variation IGNORE INDEX (somatic_feature_idx); 
+----+-------------+----------------------+------+---------------+------+-------

dbolser

DELIMITER $$
DROP   PROCEDURE IF EXISTS GetAllDistinctValuesByColumnName$$
CREATE PROCEDURE           GetAllDistinctValuesByColumnName (ColName VARCHAR(255))

BEGIN

DECLARE no_more_tables INT DEFAULT 0;
DECLARE my_table VARCHAR(255); 

dbolser

DELIMITER // 
CREATE PROCEDURE GetAllValues(ColName VARCHAR(255))
BEGIN 
SELECT
  COLUMN_NAME, TABLE_NAME
FROM
  INFORMATION_SCHEMA.COLUMNS
WHERE
  TABLE_SCHEMA = DATABASE()

dbolser

        static function isNodeNotEmpty( $node ) {
                return trim( $node[0] ) != '';
        }

        static function filterEmptyNodes( $nodes ) {
                if ( !is_array( $nodes ) ) return $nodes;
                return array_filter( $nodes, "self::isNodeNotEmpty" );
        }