[GENERAL]
description   = S. cerevisiae chromosome I
db_adaptor    = Bio::DB::GFF
db_args       = -adaptor memory
		-dir    $ENV{GBROWSE_DOCS}/sample_data/

aggregators = transcript alignment orf
plugins = BatchDumper FastaDumper RestrictionAnnotator FilterTest

# where to link to when user clicks in detailed view
link          = AUTO

# what image widths to offer
image widths  = 450 640 800 1024

# default width of detailed view (pixels)
default width = 800
default features = Genes
		   ORFs
		   tRNAs
		   Centro:overview

# The class of the feature that is used as the reference for all others
# "Sequence" is the default - change it if you use something else
reference class = Sequence

# max and default segment sizes for detailed view
max segment     = 500000
default segment = 50000

# zoom levels
zoom levels    = 50 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000

# whether to show the sources popup menu (0=false, 1=true; defaults to true)
show sources   = 1

# colors of the overview, detailed map and key
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor      = beige

# examples to show in the introduction
examples = I
	   I:80,000..120,000
	   "membrane trafficking"
	   NUT21
	   ORF:YAL063C

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone

# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
height      = 8
bgcolor     = cyan
fgcolor     = cyan
label density = 25
bump density  = 100

########################
# database configuration
########################
[yeast1:database]
db_args       = -adaptor memory
		-dir    $ENV{GBROWSE_DOCS}/sample_data/

### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks

[Centro:overview]
feature       = CEN:sgd
bgcolor       = blue
glyph         = dot
fgcolor       = black
height        = 8
point         = 1
key           = Centromeres

[Genes]
feature      = gene:sgd
data source  = sgd
track source = modENCODE
glyph        = generic
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
strand_arrow = 1
height       = 6
description  = 1
key          = Named gene

[ORFs]
feature       = ORF:sgd
glyph         = arrow
fgcolor       = red
data source   = sgd
track source  = "nicole washington" modENCODE
linewidth    = 2
height        = 6
description   = 1
key           = ORF

[CDS]
feature      = ORF:sgd
glyph        = cds
description  = 0
height       = 26
data source   = sgd flybase
track source  = "Marc Perry" modENCODE
# we need this because the yeast GFF file does not define the phase
allow_empty_phase = 1
sixframe     = 1
label        = CDS frame
key          = CDS
citation     = This track shows CDS reading frames.

[tRNAs]
feature       = tRNA:sgd
glyph         = generic
bgcolor       = lightgray
fgcolor       = black
height        = 4
stranded      = 1
description   = 1
key           = tRNAs

[Transp]
feature       = Transposon:sgd
glyph         = segments
bgcolor       = yellow
fgcolor       = black
height        = 5
stranded      = 1
key           = Transposons

[LTRs]
feature       = LTR:sgd
fgcolor       = black
glyph         = anchored_arrow
height        = 6
key           = Long Terminal Repeats

[Translation]
glyph        = translation
global feature = 1
height       = 40
fgcolor      = purple
strand       = +1
translation  = 6frame
key          = 6-frame translation

[TranslationF]
glyph        = translation
global feature = 1
height       = 20
fgcolor      = purple
strand       = +1
translation  = 3frame
key          = 3-frame translation (forward)

[DNA/GC Content]
glyph        = dna
global feature = 1
height       = 40
do_gc        = 1
strand       = both
fgcolor      = red
axis_color   = blue

[TranslationR]
glyph        = translation
global feature = 1
height       = 20
fgcolor      = blue
strand       = -1
translation  = 3frame
key          = 3-frame translation (reverse)

[ncRNA]
feature       = RNA:sgd rRNA:sgd snRNA:sgd snoRNA:sgd
fgcolor       = orange
glyph         = generic
description   = 1
key           = Noncoding RNAs
