dbolser

package Chimera;

use Moose;

use Bio::Location::Simple;
use Bio::Coordinate::Pair;
use Bio::Coordinate::Collection;


has 'chimera' =>

dbolser

#!/usr/bin/perl -w

eval 'exec /usr/bin/perl  -S $0 ${1+"$@"}'
    if 0; # not running under some shell

use strict;

use Getopt::Long;

use Bio::DB::SeqFeature::Store;

dbolser

#!/usr/bin/perl -w

use strict;

use Bio::DB::SeqFeature::Store;

my $db = Bio::DB::SeqFeature::Store->
  new( -adaptor => 'DBI::mysql',
       -dsn     => 'dbolser_004:mysql.compbio.dundee.ac.uk',
       -user => 'dbolser',

dbolser

diff --git a/Bio/SeqIO.pm b/Bio/SeqIO.pm
index 5d1722c..d3e6d90 100644
--- a/Bio/SeqIO.pm
+++ b/Bio/SeqIO.pm
@@ -370,7 +370,7 @@ sub new {
                    $class->throw("fh argument provided, but with an undefined v
                        if exists $param{'-fh'};
                    $class->throw("string argument provided, but with an undefin
-                       if exists($param{'-string'};
+                       if exists $param{'-string'};

dbolser

#!/usr/bin/perl -w

use strict;
use Bio::DB::SeqFeature::Store;

my $db = Bio::DB::SeqFeature::Store->
  new( -adaptor => 'DBI::mysql',
       -dsn     => 'my_database:mysql.mysql.host.here.ac.uk',
       -user => 'me',
       -pass => 'secret',

dbolser

# -*-Perl-*- Test Harness script for Bioperl
# $Id$


## I'm confused about the tests here, so for the sake of simplicity
## I'm going to start from scratch. Basically I just want to write a
## few tests to show up some specific bugs. Of course the right thing
## to do is to create another test file, but I don't know how to get
## SeqFeature_mysql.t to point at it (that file is automatically
## generated at build time).

dbolser

# This is the global configuration for gbrowse
# It contains setting common to all data sources as well 
# as the various constants formerly scattered amongst scripts and libraries

[GENERAL]
# overridden by environment variable GBROWSE_CONF
config_base = /homes/www-potato/httpd/conf/gbrowse2
htdocs_base = /homes/www-potato/httpd/htdocs/potato/gbrowse2
url_base    = /potato/gbrowse2
db_base     = /homes/www-potato/httpd/htdocs/potato/gbrowse2/databases

dbolser

| Biodatabase_netuser_openid     |
| Biodatabaseaccount_credentials |
| Biodatabaseaccount_requests    |
| Biodatabaseipblocks_old        |
| Biodatabaserelated_links       |
| Biodatabaseuser_openid         |
| Biodatabaseuser_sidebars       |

dbolser

mysql> select page_touched, count(*) from mb_page group by page_touched limit 20;
+----------------+----------+
| page_touched   | count(*) |
+----------------+----------+
| 2.01107052046E |      606 |
| 2.01107052047E |     1179 |
| 2.01107052048E |     1116 |
| 2.01107052049E |     1255 |
| 2.01107052092E |        2 |
| 2.01107052094E |        1 |

dbolser

mysql> show create table mb_page\G
*************************** 1. row ***************************
       Table: mb_page
Create Table: CREATE TABLE `mb_page` (
  `page_id` int(8) unsigned NOT NULL auto_increment,
  `page_namespace` int(11) NOT NULL default '0',
  `page_title` varchar(255) character set utf8 collate utf8_bin NOT NULL default '',
  `page_restrictions` tinyblob NOT NULL,
  `page_counter` bigint(20) unsigned NOT NULL default '0',
  `page_is_redirect` tinyint(1) unsigned NOT NULL default '0',