[GENERAL]
description = test implementation of chado
database = main
plugins = AttributeHiliter
# 'region' or 'contig' would be other typical choices,
# remember that in chado, the ref class must be part of
# SOFA (as must all feature types)
reference class = chromosome
#Do not use aggregators with the chado adaptor
#aggregators =
# examples to show in the introduction
examples = YAL031C
YCR02*
ChrV:100000-120000
# "automatic" classes to try when an unqualified identifier is given
automatic classes = gene
#################################
# database definitions
#################################
[main:database]
db_adaptor = Bio::DB::Das::Chado
db_args = -dsn dbi:Pg:dbname=chado;host=localhost;port=5432
-user nobody
-pass blah
-srcfeatureslice 1
-inferCDS 1
-organism "Saccharomyces cerevisiae"
# another option includes -fulltext 1 but requires running a helper
# script to prep the database first: gmod_chado_fts_prep.pl
# See 'perldoc Bio::DB::Das::Chado' for more information.
### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks
[Genes]
feature = gene
glyph = arrow
base = 1
fgcolor = red
height = 5
linewidth = 2
key = Named gene
[Transcript]
feature = mRNA
glyph = transcript
key = mRNA
[CDS]
feature = gene
sub_part = CDS
glyph = cds
height = 20
key = CDS
[tRNA]
feature = tRNA
key = tRNA
[SNP]
feature = SNP
glyph = triangle
key = SNP
[STS]
feature = STS
key = STS
[Landmarks:overview]
feature = region:landmark
glyph = generic
fgcolor = green
key = Landmarks