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<opt
name="gbrowseconf"
date="20040826"
db_adaptor_class = "Bio::DB::GFF"
db_adaptor = "lucene"
db_dsn = "${outputpath}/lucene/"
db_user = "flybase"
db_password = " "
db_adaptor_class2 = "Bio::DB::Das::Chado"
db_adaptor1 = "dbi::mysql"
db_adaptor2 = "dbi::Pg"
>
<!-- need to call XML::Simple w/ ${variables} below in doc
${species} ${relfull} ${date}
${datapath}
${default_location}
${chromosomes} == ${examples} ??
readConfig( 'gbrowseconfig', { Variables => \%featvars });
-->
<title>Gbrowse conf generator</title>
<about>
</about>
<!-- add gbrowse.conf file parts here; as per blastfiles.doc -->
<doc name="dummy"></doc>
<doc name="gbrowse" path="gff/gbrowse.conf">
<!-- no content tag here -->
<header title="header"><![CDATA[
# generated gbrowse config
[GENERAL]
description = ${species} ${rel}
## option GFF xxx adaptor
db_adaptor = ${db_adaptor_class}
db_args = -adaptor ${db_adaptor}
-dsn ${db_dsn}
user = ${db_user}
passwd = ${db_password}
## option Pg::Chado adaptor
# db_adaptor = Bio::DB::Das::Chado
# database = ${db_dsn}
## option dbi::mysql adaptor
# adaptor = dbi::mysql
# database = ${db_dsn}
## option lucene adaptor
# db_adaptor = lucene
# db_dsn = "${outputpath}/lucene/"
default_name = ${default_location}
default_range = 1-500000
examples = ${default_location} ${examples}
header =
<h1>Genome Browser: <i>${species}</i>
<br><small>Release ${rel}; ${date}</small>
</h1>
footer = <hr>
<table width="100%">
<TR>
<TD align="LEFT" class="databody">
For the source code for this browser, see the <a href="http://www.gmod.org">
Generic Model Organism Database Project.</a>
</TD>
</TR>
</table>
<hr>
<pre>$Id: gbrowseconf.xml,v 1.5 2007-10-17 01:01:29 dongilbert Exp $</pre>
plugins = BatchDumper TextMapDumper FeatureFastaDumper FastaDumper GFFDumper
aggregators = processed_transcript alignment
#fixme ...
uploads = 1
#fixme ...
default features = gene scaffold
# Web site configuration info
stylesheet = /gbrowse/gbrowse.css
buttons = /gbrowse/images/buttons
tmpimages = /gbrowse/tmp
help = /gbrowse/
# max and default segment sizes for detailed view
max segment = 1000001
default segment = 100000
# where to link to when user clicks in detailed view
link = AUTO
title = sub { my $f= shift;
return $f->method .":". $f->info . " ". $f->seq_id .':'.$f->start."..".$f->end;
}
zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000
# colors of the overview, detailed map and key
overview units = M
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
#panel property
pad_left = 20
pad_right = 30
key_style = between
key bgcolor = whitesmoke
grid = 1
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone
language = en
image widths = 450 640 800 950 1024
default width = 800
# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =
# Default glyph settings
[TRACK DEFAULTS]
glyph = generic
height = 8
bgcolor = cyan
fgcolor = cyan
label density = 25
bump density = 100
overview label density = 160
### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks
[DNA/GC Content]
glyph = dna
global feature = 1
height = 40
do_gc = 1
fgcolor = red
axis_color = blue
]]></header>
<footer title="footer"><![CDATA[
]]></footer>
</doc>
<!-- ============ GENERIC is template for unconfigured features =========== -->
<fdef name="GENERIC"><![CDATA[
[GENERIC]
feature = GENERIC
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = GENERIC
citation = GENERIC
#category = Analysis
]]></fdef>
<!-- ============ Genomic features =========== -->
<fdef name="cytoband"><![CDATA[
[cytoband]
feature = cytoband
glyph = revcomp_arrow
both = 1
label_align = center
fgcolor = black
bgcolor = black
linewidth = 2
label = 1
label density = 10000
bump = 0
bump density = 0
key = Cytologic band
category = Genomic
citation = Cytological bands on the polytene chromosomes
link = sub { my $f=shift; my $u=$ENV{REQUEST_URI};
my $r= $f->ref.":".$f->to_FTstring;
$u =~ s/\?.*$//; $u .= '?name='.$r.";doexpand=1";
return $u;
}
]]></fdef>
<fdef name="dna"><![CDATA[
[dna]
feature = source
glyph = dnabases
draw_dna = 1
strand = forward
label = 0
label density = 0
key = DNA sequence
category = Genomic
link =
]]></fdef>
<fdef name="gene" feature="gene mRNA"><![CDATA[
[gene]
feature = gene mRNA
glyph = transcript2
bgcolor = lightblue
fgcolor = blue
secondary = mRNA
secondary_bgcolor = mediumblue
secondary_fgcolor = mediumblue
highlight_color = red
higlighted = 1
label = 1
label density = 50
key = Gene Model
category = Genomic
citation = Gene and mRNA (transcript) features
]]></fdef>
<fdef name="CDS"><![CDATA[
[CDS]
feature = CDS
glyph = segments
stranded = 1
translation = 1frame
bgcolor = palegoldenrod
fgcolor = goldenrod
label = 1
key = CDS
citation = Protein coding sequence
category = Genomic
]]></fdef>
<fdef name="pseudogene"><![CDATA[
[pseudogene]
feature = pseudogene
glyph = segments
strand_arrow = 1
fgcolor = orange
label = 1
key = Pseudogene
category = Genomic
]]></fdef>
<fdef name="tRNA"><![CDATA[
[tRNA]
feature = tRNA
glyph = transcript2
label = 1
stranded = 1
bgcolor = white
fgcolor = black
curatedexon = slateblue
fontcolor = slateblue
key = tRNA
category = Genomic
]]></fdef>
<fdef name="noncodingRNA" feature="ncRNA rRNA snoRNA snRNA miscRNA"><![CDATA[
[ncRNA]
feature = ncRNA rRNA snoRNA snRNA miscRNA
glyph = transcript2
bgcolor = peachpuff
stranded = 1
key = Non-coding RNAs
citation = Non-coding RNAs: ncRNA rRNA snoRNA snRNA miscRNA
category = Genomic
]]></fdef>
<fdef name="transposable_element"><![CDATA[
[transposable_element]
feature = transposable_element
bgcolor = magenta
fgcolor = magenta
label = 1
glyph = anchored_arrow
key = Natural transposon
citation = Natural transposon
category = Genomic
]]></fdef>
<fdef name="transposable_element_insertion_site"><![CDATA[
[transposable_element_insertion_site]
feature = transposable_element_insertion_site
glyph = pinsertion
bgcolor = darkturquoise
fgcolor = darkturquoise
bump = 1
label = 0
key = Transgene insertion site
citation = Transgene insertion site
category = Genomic
]]></fdef>
<!-- ============ Misc. Genomic features =========== -->
<fdef name="polyA_site"><![CDATA[
[polyA_site]
feature = polyA_site
strand_arrow = 1
bgcolor = lightslategray
fgcolor = lightslategray
key = polyA_site
citation = polyA_site
category = Miscellany Genomic
]]></fdef>
<fdef name="point_mutation"><![CDATA[
[point_mutation]
feature = point_mutation
bgcolor = lightslategray
fgcolor = lightslategray
key = point_mutation
citation = point_mutation
category = Miscellany Genomic
]]></fdef>
<fdef name="protein_binding_site"><![CDATA[
[protein_binding_site]
feature = protein_binding_site
strand_arrow = 1
bgcolor = lightslategray
fgcolor = lightslategray
key = protein_binding_site
citation = protein_binding_site
category = Miscellany Genomic
]]></fdef>
<fdef name="rescue_fragment"><![CDATA[
[rescue_fragment]
feature = rescue_fragment
strand_arrow = 1
bgcolor = lightslategray
fgcolor = lightslategray
key = rescue_fragment
citation = rescue_fragment
category = Miscellany Genomic
]]></fdef>
<fdef name="mature_peptide"><![CDATA[
[mature_peptide]
feature = mature_peptide
glyph = segments
strand_arrow = 1
bgcolor = palegoldenrod
fgcolor = orange
label = 1
key = mature_peptide
citation = mature_peptide
category = Miscellany Genomic
]]></fdef>
<fdef name="signal_peptide"><![CDATA[
[signal_peptide]
feature = signal_peptide
glyph = segments
strand_arrow = 1
bgcolor = palegoldenrod
fgcolor = orange
label = 1
key = signal_peptide
citation = signal_peptide
category = Miscellany Genomic
]]></fdef>
<fdef name="enhancer"><![CDATA[
[enhancer]
feature = enhancer
strand_arrow = 1
bgcolor = lightslategray
fgcolor = lightslategray
key = enhancer
citation = enhancer
category = Miscellany Genomic
]]></fdef>
<fdef name="aberration_junction"><![CDATA[
[aberration_junction]
feature = aberration_junction
strand_arrow = 1
bgcolor = lightslategray
fgcolor = lightslategray
key = aberration_junction
citation = aberration_junction
category = Miscellany Genomic
]]></fdef>
<fdef name="regulatory_region"><![CDATA[
[regulatory_region]
feature = regulatory_region
strand_arrow = 1
bgcolor = lightslategray
fgcolor = lightslategray
key = regulatory_region
citation = regulatory_region
category = Miscellany Genomic
]]></fdef>
<fdef name="sequence_variant"><![CDATA[
[sequence_variant]
feature = sequence_variant
strand_arrow = 1
bgcolor = lightslategray
fgcolor = lightslategray
key = sequence_variant
citation = sequence_variant
category = Miscellany Genomic
]]></fdef>
<fdef name="DNA_motif" feature="DNA_motif RNA_motif"><![CDATA[
[DNA_motif]
feature = DNA_motif RNA_motif
bgcolor = plum
fgcolor = plum
secondary = RNA_motif
secondary_bgcolor = mediumseagreen
secondary_fgcolor = mediumseagreen
strand_arrow = 1
bump = 1
label = 0
key = DNA / RNA motif
citation = DNA_motif and RNA_motif
category = Miscellany Genomic
]]></fdef>
<!-- ============ Analysis =========== -->
<fdef name="transcription_start_site"><![CDATA[
[transcription_start_site]
feature = transcription_start_site
glyph = promoter
bgcolor = purple
fgcolor = purple
bump = 1
label = 0
key = Promoter prediction
citation = Transcription promoter prediction
category = Analysis
]]></fdef>
<fdef name="processed_transcript"><![CDATA[
[processed_transcript]
feature = processed_transcript
glyph = processed_transcript
bgcolor = plum
fgcolor = plum
height = 4
bump = 1
label = 0
key = Processed transcript
citation = processed_transcript
category = Analysis
]]></fdef>
<fdef name="protein"><![CDATA[
[protein]
feature = protein
bgcolor = salmon
fgcolor = salmon
height = 3
strand_arrow = 1
bump = 1
label = 1
key = Protein BLAST alignment
citation = protein from BLAST alignments
category = Analysis
]]></fdef>
<fdef name="repeat_region"><![CDATA[
[repeat_region]
feature = repeat_region
bgcolor = darkorchid
fgcolor = darkorchid
height = 3
connector = solid
bump = 1
strand_arrow = 0
label = 0
key = Repeat region
citation = repeat_region
category = Analysis
link =
]]></fdef>
<fdef name="mRNA_genscan"><![CDATA[
[mRNA_genscan]
feature = mRNA_genscan
glyph = segments
strand_arrow = 1
bgcolor = tan
fgcolor = brown
connector = solid
bump = 1
label = 0
key = Genscan prediction
citation = Genscan (gene prediction)
category = Analysis
]]></fdef>
<fdef name="mRNA_piecegenie"><![CDATA[
[mRNA_piecegenie]
feature = mRNA_piecegenie
glyph = segments
strand_arrow = 1
bgcolor = yellow
fgcolor = brown
connector = solid
bump = 1
label = 0
key = Genie prediction
citation = PieceGenie (gene prediction)
category = Analysis
]]></fdef>
<fdef name="match_fgenesh"><![CDATA[
[match_fgenesh]
feature = match_fgenesh
glyph = segments
strand_arrow = 1
bgcolor = tan
fgcolor = brown
connector = solid
bump = 1
label = 0
key = fgenesh prediction
citation = match_fgenesh (gene prediction)
category = Analysis
]]></fdef>
<fdef name="match_HDP"><![CDATA[
[match_HDP]
feature = match_HDP
glyph = segments
strand_arrow = 1
bgcolor = yellow
fgcolor = brown
connector = solid
bump = 1
label = 0
key =HDP prediction
citation = HDP
category = Analysis
]]></fdef>
<fdef name="match_RNAiHDP"><![CDATA[
[match_RNAiHDP]
feature = match_RNAiHDP
glyph = segments
strand_arrow = 1
bgcolor = tan
fgcolor = brown
connector = solid
bump = 1
label = 0
key = RNAiHDP prediction
citation = RNAiHDP
category = Analysis
]]></fdef>
<fdef name="tRNA_trnascan"><![CDATA[
[tRNA_trnascan]
feature = tRNA_trnascan
glyph = transcript2
bgcolor = yellow
fgcolor = brown
connector = solid
bump = 1
label = 0
key = tRNAscan prediction
citation = tRNAscan (tRNA prediction)
category = Analysis
]]></fdef>
<fdef name="transposable_element_pred"><![CDATA[
[transposable_element_pred]
feature = transposable_element_pred
bgcolor = tan
fgcolor = brown
label = 1
glyph = anchored_arrow
key = Transposon prediction
citation = Transposon prediction
category = Analysis
]]></fdef>
<!-- ============ Genome reagents =========== -->
<fdef name="oligonucleotide"><![CDATA[
[oligonucleotide]
feature = oligonucleotide
glyph = generic
bgcolor = tomato
fgcolor = tomato
height = 4
bump = 0
bump density = 1
label = 0
label density = 0
key = Affy Oligo
citation = oligonucleotide
category = Genome reagents
]]></fdef>
<fdef name="EST" feature="EST cDNA_clone"><![CDATA[
[EST]
feature = EST cDNA_clone
glyph = segments
strand_arrow = 1
bgcolor = lightgreen
fgcolor = green
secondary = cDNA_clone
secondary_bgcolor = mediumseagreen
secondary_fgcolor = mediumseagreen
key = cDNA + EST
citation = cDNA_clone and EST
category = Genome reagents
link = sub {
my $v=shift->name(); $v=~s/[:.].*(prime|contig).*$//; $v=~s/^(GB)[:]//;
return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$v;
}
]]></fdef>
<fdef name="blast"><![CDATA[
[blast]
feature = blast
glyph = alignment
bgcolor = darkorchid
fgcolor = darkorchid
bump = 1
label = 1
key = Blast hit
height = 8
citation = BLAST alignment hit
category = "hidden"
]]></fdef>
<fdef name="BAC"><![CDATA[
[BAC]
feature = BAC
glyph = extending_arrow
no_arrows = 1
base = 0
bgcolor = lightslategray
fgcolor = lightslategray
linewidth = 2
bump = 1
label = 1
key = Tiling BAC
citation = BAC
category = Genome reagents
]]></fdef>
<!--
name="golden_path"
alt_name0 = "golden_path_region"
alt_name1 = "golden_path_fragment"
alt_name2 = "databank_scaffold"
alt_name3 = "scaffold"
alt_name4 = "supercontig"
-->
<fdef name="scaffold" feature="scaffold golden_path_fragment segment"><![CDATA[
[scaffold]
## aug04 - renamed to SO equivalent golden_path;
## sep04 - golden_path_fragment is better, or supercontig ?
feature = scaffold golden_path_fragment
glyph = anchored_arrow
no_arrows = 1
base = 0
fgcolor = black
bgcolor = black
linewidth = 2
bump = 1
label = 1
height = 4
key = GenBank Scaffold
citation = genbank submission unit, a golden_path_fragment
category = Genome reagents
]]></fdef>
</opt>
|