############ Tim's Database Helper Configuration File #############

# Settings for connecting to a relational database

### Default Settings ###

# These are default settings that are shared by all databases.

# The user and password keys are for authenticating to the database.

# The adaptor key specifies the module driver for connecting to the relational 
# database containing the Bio::DB::SeqFeature::Store database. Acceptable 
# values include DBI::mysql, DBI::Pg, or DBI::SQLite. 

# The dsn key defines the string for connecting to the database. For example, 
# to connect to a mysql database 'genome' on localhost through a socket
# 	dbi:mysql:genome
# to connect to a remote mysql database
# 	dbi:mysql:host=127.0.0.1;port=3306;database=genome
# The dsn_prefix key simply drops the database name, allowing it to be used 
# with any database name.

# See the documentation for Bio::DB::SeqFeature::Store for syntax of 
# adaptor and dsn_prefix keys. 

# The reference_sequence_type key is to describe the GFF type for reference 
# sequences in the genome. Values could include chromosome, sequence, 
# scaffold, contig, etc. This is used by tim_db_helper::get_new_genome_list() 
# when getting the list of reference sequences.

# The source_exclude key provides a list of common source tags that may be 
# excluded when using the tim_db_helper::get_dataset_list() function. This 
# is used to generate a list, for example, of microarray datasets stored in 
# the database for interactive choosing. Features which have one of these 
# sources would not be included in the list. It's nice sometimes not to see 
# every possible feature in the database. 

# The window is the size in bp when generating genomic window intervals. It 
# is used by the tim_db_helper::get_new_genome_list() function.

[default_db]
user                     = nobody
pass                     = hello
adaptor                  = DBI::mysql
dsn_prefix               = dbi:mysql:
reference_sequence_type  = chromosome
source_exclude           = SGD, GeneDB, Ensembl, UCSC, refSeq, ensGene, rmsk
window                   = 500

# Multiple database sections may be included. Simply name the section after the 
# name of the database. Database specific keys may be included, and missing 
# keys will default to the default_db values. Here is an example for the 
# database named example

[example]
user                     = me
pass                     = secret
dsn                      = dbi:mysql:host=127.0.0.1;port=3306;database=example



### Feature Alias Lists ###
# These are aliases for one or more GFF feature types when searching 
# for these features in the database.
# Specify as either the GFF "type" or "type:source". These represent GFF 
# columns 3 and 2:3, respectively.

[features]
gene        = gene, ORF, ncRNA, snRNA, snoRNA
rna         = ncRNA, snRNA, snoRNA, tRNA
orf         = gene, ORF
repeat      = repeat_region, long_terminal_repeat, transposable_element_gene, LTR_retrotransposon



### Exclude Tags ###
# Some features in the database you simply don't want in your list. For 
# example, in the cerevisiaie GFF3 annotation, dubious genes are included 
# as gene features, but have the GFF "orf_classification" tag value of 
# "Dubious". I don't want these features. Ever. These tags are checked 
# using the tim_db_helper::get_new_feature_list() function.

# Specify the tag key and the tag value(s) to be excluded

[exclude_tags]
orf_classification    = Dubious



### Applications ###
# Some biotoolbox scripts require helper programs. Enter the name of the 
# helper program and the full path of its location. Executable programs 
# may also be automatically found in the system path.

[applications]
wigToBigWig      = /usr/local/bin/wigToBigWig
java             = /usr/bin/java
Bar2Gr           = /Applications/USeq/Apps/Bar2Gr