[GENERAL]
description   = Yeast chromosomes 1+2 (basic)
database      = scaffolds

initial landmark = chrI:143000..180000
plugins       = FilterTest RestrictionAnnotator TrackDumper FastaDumper
autocomplete  = 1

default tracks = Genes
		   ORFs
		   tRNAs
		   CDS
		   Transp
		   Centro:overview
		   GC:region

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

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

#################################
# database definitions
#################################

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    $DATABASES/yeast_scaffolds
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    $DATABASES/yeast_chr1+2
search options = default +autocomplete

# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
database    = annotations
height      = 8
bgcolor     = cyan
fgcolor     = black
label density = 25
bump density  = 100
show summary  = 99999  # go into summary mode when zoomed out to 100k

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

[Centro:overview]
feature       = centromere
bgcolor       = blue
glyph         = dot
fgcolor       = black
height        = 8
point         = 1
show summary  = 0   # no summary of this one
key           = Centromeres

[tRNA:overview]
feature       = tRNA
glyph         = generic
bgcolor       = lightgray
fgcolor       = black
height        = 4
stranded      = 1
description   = 1
show summary  = 0   # no summary of this one
key           = tRNAs

[GC:region]
glyph        = dna
global feature = 1
database     = scaffolds
height       = 40
gc_window    = auto
do_gc        = 1
strand       = both
fgcolor      = red
axis_color   = blue
show summary  = 0   # no summary of this one
key          = GC Content

[Genes]
feature      = gene
glyph        = gene
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
label        = sub { my $f = shift;
                     my $name = $f->display_name;
                     my @aliases = sort $f->attributes('Alias');
                     $name .= " (@aliases)" if @aliases;
		     $name;
  } 
height       = 6
description  = 0
key          = Named gene

[CDS]
feature      = gene
glyph        = cds
description  = 0
height       = 26
sixframe     = 1
label        = sub {shift->name . " reading frame"}
key          = CDS
citation     = This track shows CDS reading frames.

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

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

[LTRs]
feature       = long_terminal_repeat
fgcolor       = black
glyph         = anchored_arrow
height        = 6
key           = Long Terminal Repeats

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

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

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

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

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