fly_yakuba.conf

[GENERAL]
description   = D. yakuba modENCODE (FlyBase R1.3) (test)
database      = dyakuba
plugins       = FastaDumper RestrictionAnnotator SequenceDumper



initial landmark = 2L:193000..200999
default features = Genes

# examples to show in the introduction
examples = 2R:18159030..18178930
           3L:8148750..8166749
           X:73501..94501
           4:638000..654999


header =
  <table style="border-bottom:5px groove blue;margin-bottom:10px;width:98%">
    <tr>
      <td valign=top>
        <a href="http://www.modencode.org">
          <img src="/images/fly_small.png"
               border=0 alt="modENCODE logo fly" />
        </a>
      </td>
      <th valign=middle>
        <span style="font:arial;font-size:18pt"><i>D. yakuba</i> Genome Browser</span>
      </th>
      <td width="20%"></td>
    </tr>
  </table>



# "automatic" classes to try when an unqualified identifier is given
automatic classes = CDS
pad_left          = 180
truecolor         = 1
autocomplete      = 1

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

[dyakuba:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn    dyakuba
                -user   nobody
search options = exact +autocomplete

[white:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn    white
                -user   nobody
search options = exact


# Default glyph settings
[TRACK DEFAULTS]
glyph         = generic
database      = dyakuba
height        = 8
bgcolor       = lightgrey
fgcolor       = black
label density = 100
bump density  = 500
feature limit = 500
discoverable  = 1
link          = AUTO

# Ucsc plugin configuration
#[UcscPlugin:plugin]
#db = dm3
#user = viewer
#pass = viewer
#seq_prefix = chr
#split_prefix = chr

#[UcscChain:plugin]
#default_enable = chainDp3

#[UcscNet:plugin]
#default_enable = netDroAna2 netDp3

#[UcscConservation:plugin]
#default_enable = multiz15way

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

[Genes:100000]
glyph        = generic
bump         = 0
maxdepth     = 1
stranded     = 1
label        = 0
description  = 0

[Genes]
feature      = gene:FlyBase
               pseudogene:FlyBase
glyph        = gene
height       = 8
bgcolor      = sub {
                 my $f = shift;
                 return 'white' if $f->primary_tag eq 'pseudogene';
                 return $f->strand < 1 ? 'turquoise' : 'violet';
               }
utr_color    = silver
label        = sub {
                my $f = shift;
                my $dn = $f->display_name;
		$dn =~ s!Dyak\W!!;
                my @aliases = $f->each_tag_value('Alias');
                foreach (@aliases) {
                   return "$dn ($_)" if /^\w+-\d+/;
                }
                return $dn;
        }
filter       = sub {
                 my @subf = eval{shift->get_SeqFeatures('mRNA')};
                 return @subf > 0;
              }
description  = sub {
        my $f = shift;
        my @subf = eval{$f->get_SeqFeatures};
        my $note;
        for my $sf (@subf) {
           next unless $sf->primary_tag =~ /RNA|pseudo/;
           $note ||= join '; ',$sf->each_tag_value('Note');
        }
        $note =~ s!Dyak\W!!;
        $note;
  }
link         = sub {my $n = shift->name;
                    $n =~s/Dyak\W//;
                    return "http://www.flybase.org/cgi-bin/uniq.html?species=Dyak\&field=SYN\&db=fbgn\&context=$n\&caller=quicksearch";}
label_transcripts =  sub { return shift->primary_tag eq 'mRNA' }
das category = transcription
key          = FlyBase Genes
category     = Gene Models and Predictions
citation     = Annotated gene models from FlyBase Release R1.2; Feb 2009.

[TranslationF]
glyph        = translation
global feature = 1
height       = 20
fgcolor      = purple
start_codons = 0
strand       = +1
arrow_height = 2
translation  = 3frame
category     = Sequence
key          = 3-frame translation (forward)
citation     = This track shows the position of stop codons at low magnifications,
        and the 3-frame translation at high magnifications.  Only the forward strand
        is shown.

[DNA/GC Content] 
glyph          = dna
global feature = 1
strand         = both
gc_window      = auto
height         = 40
fgcolor        = red
key            = GC Content
category       = Sequence
citation       = This track show the %GC of the displayed sequence region.  When zoomed in close enough, the DNA sequence is displayed

[TranslationR]
glyph        = translation
global feature = 1
height       = 20
fgcolor      = blue
strand       = -1
start_codons = 0
arrow_height = 2
translation  = 3frame
category     = Sequence
key          = 3-frame translation (reverse)
citation     = This track shows the position of stop codons at low magnifications,
        and the 3-frame translation at high magnifications.  Only the reverse
        strand is shown.



# Some reservations about putting tRNAs and ncRNAs in a category other than genes
#[cDNA]
#feature       = cDNA_match
#filter        = sub {shift->source_tag ne 'dm3'}
#glyph         = segments
#label         = 1
#database      = imported
#category      = Gene Expression: ESTs and mRNAs
#draw_target   = 1
#show_mismatch = 1
#ragged_start  = 1
#height        = 5
#bgcolor       = limegreen
#fgcolor       = black
#connector     = solid
#key           = full length cDNAs
#citation      = Full Insert cDNAs sequenced by the Berkeley Drosophila Genome Project (http://www.fruitfly.org)


[miRNA:500000]
label            = 0

[miRNA]
feature          = miRNA:FlyBase
glyph            = generic
strand_arrow     = 1
bgcolor          = wheat
fgcolor          = black
height           = 5
description      = 1
label            = sub {my $n = shift->name;
                        $n =~ s/Dyak\W//;
                        return $n;}
key              = FlyBase miRNAs
category         = non-modENCODE Reference Data:Non-coding RNAs from FlyBase
citation         = miRBase data from sanger miRNA database (more frequently updated than FlyBase)

[ncRNA]
feature          = gene:FlyBase
filter           = sub { shift->name =~ /ncRNA|snoRNA|snRNA/ }
glyph            = generic
strand_arrow     = 1
bgcolor          = white
fgcolor          = black
label            = sub {my $n = shift->name;
                        $n =~ s/Dyak\W//;
                        return $n;}
height           = 5
description      = 1
key              = FlyBase non-coding RNAs
category         = non-modENCODE Reference Data:Non-coding RNAs from FlyBase
citation         = miRBase data from sanger miRNA database (more frequently updated than FlyBase)


[TRNA:500000]
label            = 0

[TRNA]
feature          = gene:FlyBase
filter           = sub { shift->name =~ /tRNA/ }
glyph            = generic
bgcolor          = white
fgcolor          = black
height           = 5
description      = 0
label            = sub {my $n = shift->name;
                        $n =~ s/Dyak\W//;
                        return $n;}
key              = tRNAs
category         = non-modENCODE Reference Data:Non-coding RNAs from FlyBase


### MODENCODE TRACKS:

## CELNIKER TRACKS

#include celniker.dyak_conf/*.conf

## HENIKOFF TRACKS

##include henikoff.dm_conf/*.conf

## KARPEN TRACKS

##include karpen_conf/*.conf

## LAI TRACKS

##include lai_conf/*.conf

## MACALPINE TRACKS

##include macalpine_conf/*conf

## WHITE TRACKS

##include white_conf/*.conf