# gbrowse config file for flybase D.pseudo
# d.gilbert, jul04
[GENERAL]
description = D. pseudoobscura Genome (R1.04)
#datapath = /data/genomes/dpse/gnomap
#datapath = /genomes/Drosophila_pseudoobscura/dpse_r10_20041216/gnomap
datapath = /genomes/Drosophila_pseudoobscura/current/gnomap
organism = D. pseudoobscura
# synteny tests; 04oct
synteny_idmap = dmel-synt-idmap.tsv
synteny_org = D. melanogaster
##synteny_src = dmel
synteny_src = dmel_r322
header =
FlyBase Genome Browser: D. pseudoobscura
Release 1.04, Dec 2004
NOTE: "Chromosome U" is an unordered collection
of contigs that have not been located to a chromosome or ultracontig.
These are artificially collected as "chromosome U" for display.
Locations on U are not useful between contigs.
footer =
Adapted from GBrowse of the
Generic Model Organism Database Project.
default_name = 2:100000-200000
default_range = 1-500000
# examples to show in the introduction
# examples =
# 2: 3:
2:3500000..3800000
# 4_group1: 4_group2: 4_group3: 4_group4: 4_group5:
# XL_group1a: XL_group1e: XL_group3b: XL_group3a:
# XR_group3a: XR_group5: XR_group6: XR_group8: XR_group9:
chromosomes =
2: 2_groupMISC:
3: 3_groupMISC:
4_group1: 4_group2: 4_group3: 4_group4: 4_group5:
4_groupMISC:
5_groupMISC:
XL_group1a: XL_group1e: XL_group3a: XL_group3b:
XL_groupMISC:
XR_group3a: XR_group5: XR_group6: XR_group8: XR_group9:
XR_groupMISC:
U:
adaptor = flybase::gmod::FFFdb
plugins = BatchDumper TextMapDumper FeatureFastaDumper FastaDumper GFFDumper
default features = rev_ruler gene orthologous_region syntenic_region
primary_feature = gene
# scale_feature = cytoband
# ignore these for now - NO?
# feature_skip = cytoabs cytodef cytodup cytogene cytoins cytoinv cytotloc cytowalk
dumpviews = FastA GenBank GFF FFF
# dumpviews =
dataviews = "Default" "Collapse All" "Expand All"
# "Labelling On"
uploads = 1
# Web site configuration info
# stylesheet = /templates/gbrowse.css
# help = /maps/gbrowse
help = /common/perl/gbrowse_fb/htdocs
stylesheet = /common/perl/gbrowse_fb/gbrowse.css
buttons = /common/perl/gbrowse_fb/images/buttons
tmpimages = /tmp/gbrowse_fb
# bac_insitu_pic = /images/lk/bac_insitu_pic
# max num bac image display (set to 0 to disable)
max bac pic = 0
# max and default segment sizes for detailed view
max segment = 1000001
default segment = 100000
## base range to expand around gene given ID lookup
# expand_by = 60000
expand_by = 20000
zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000
#searchhelp =
#Search using Chromosome:base_start..end or FlyBase Gene ID.
searchhelp = To find Dmel gene orthologs, use Find [Dmel\Gene_Symbol]
with gene symbols prefixed by 'Dmel\', e.g.
'Dmel\Ubx',
'Dmel\cnn'
searchitem = Find
\n
\n
\n
#panel property
pad_left = 20
pad_right = 30
key_style = between
key bgcolor = whitesmoke
overview bgcolor = whitesmoke
grid = 1
# put reversed features on same track or below ?
mix_strand = 1
# # where to link to when user clicks in detaild view
## this dummy link allows title display; otherwise no url title :(
# link = "#"
# generic FB link - should work if FB id is in data
link = sub {
my $f= shift; my ($d);
$d= $f->primary_id() if $f->can('primary_id');
$d= $f->source() unless($d);
if ($d =~ /(FB\w\w\d+)/){ return '/cgi-bin/fbidq.html?'.$1; }
elsif ($d =~ /^(GA|CG|CR|TE)\d+/ ){ return '/cgi-bin/fbidq.html?'.$d; }
($d)= $f->each_tag_value('note'); # best ids now 'hidden' in notes, Dbxref
if ($d =~ /(FB\w\w\d+)/) { return '/cgi-bin/fbidq.html?'.$1; }
elsif ($d =~ /((GA|CG|CR|TE)\d+)/ ){ return '/cgi-bin/fbidq.html?'.$1; }
if ($f->name()) { return '/cgi-bin/fbsymq.html?'.$f->name(); } # or fbannq.html?name
}
## NOTE: this is used by TextMapDumper plugin
# my $link = $browser->config->code_setting($label,'dbx_link');
# $link = $browser->config->code_setting(general=>'dbx_link') unless defined $link;
dbx_link = sub {
my $dbx= shift; my $f= shift; #?
my $r='';
foreach my $x (split(/[,;]\s*/,$dbx)) {
my($h,$v);
my($db,$ac)= split/:/,$x,2;
if ($x =~ /(FB\w\w\d+)/) { $v=$1; $h= '/cgi-bin/fbidq.html?'.$v; }
elsif ($db =~ /FlyBase/i) { $v=$ac; $h= '/cgi-bin/fbsymq.html?'.$ac; }
elsif ($db eq 'GB_protein') {
$v= $ac;
$h= 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenBank&tool=FlyBase&term='.$ac;
}
elsif ($db eq 'GB') {
$v= $ac;
$h= 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$ac;
}
elsif ($db eq 'GO') {
$v= $ac;
$h= '/cgi-bin/goreport?id='.$ac;
}
if ($h && $v) { $r.= ''.$v.', '; }
else { $r.= $x.', '; }
}
return $r;
}
# title = sub { my $f=shift; return ($f->name())? $f->name(): "" ; }
# make_title in Browser should be doing this, but get only "Gene" == class?
# the perl syntax ->method||'' was causing failure !
title = sub { my $f= shift;
return $f->class .":". $f->info . " ". $f->seq_id .':'.$f->start."..".$f->end;
}
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene
# Default glyph settings
glyph = generic
height = 5
bgcolor = palegoldenrod
fgcolor = cyan
boxcolor = blue
label density = 20
bump density = 50
overview label density = 160
image widths = 450 640 800 950 1024
# default width of detailed view (pixels)
default width = 800
width = 800
#---------- end [GENERAL] ------------------------
##? these sections seem to work only per GMOD->track not per feature ??
# bperl equates [label] with feature type
[rev_ruler]
glyph = ruler_arrow
label = 0
no_53_label = 1
label_align = center
tick = 1
no_tick_label = 0
units = K
link =
key = Base ruler
nodump = 1
keygroup = " Genomic features"
[dna]
feature = source
glyph = dnabases
draw_dna = 1
strand = forward
label = 0
label density = 0
nodump = 1
key = DNA sequence
keygroup = " Genomic features"
link =
[dnarev]
feature = source
glyph = dnabases
draw_dna = 1
nodump = 1
strand = reverse
label = 0
label density = 0
key = DNA reverse complement
keygroup = " Genomic features"
link =
[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
keygroup = " Genomic features"
citation = Gene and mRNA (transcript) features (annotation DB ; Chado)
NOTNOW_link = sub {
my $f= shift; my ($d);
$d= $f->primary_id() if $f->can('primary_id');
$d= $f->source() unless($d);
if ($d =~ /(FB\w\w\d+)/){ return '/cgi-bin/fbidq.html?'.$1; }
elsif ($d =~ /^(GA)\d+/ ){ return '/cgi-bin/fbidq.html?'.$d; }
elsif ($d =~ /^(C[GR]|TE)\d+/ ){ return '/cgi-bin/fbidq.html?'.$d; }
($d)= $f->each_tag_value('note'); # best ids now 'hidden' in notes, Dbxref
if ($d =~ /(FB\w\w\d+)/) { return '/cgi-bin/fbidq.html?'.$1; }
if ($f->name()) { return '/cgi-bin/fbsymq.html?'.$f->name(); } # or fbannq.html?name
}
NOTrename = sub { my $f= shift; my $tn= $f->info;
my ($nt)= $f->each_tag_value('note');
if ($nt =~ m/ortholog\w+=FlyBase:([^;,]+)/) { $tn .= " Dmel\\".$1; }
return $tn;
}
title = sub { my $f= shift;
my $t= $f->class .":". $f->info;
my ($nt)= $f->each_tag_value('note');
if ($nt =~ m/ortholog\w+=FlyBase:([^;,]+)/) { $t .= " Dmel\\".$1; }
$t .= " ". $f->seq_id .':'.$f->start."..".$f->end;
return $t;
}
[CDS]
feature = CDS
# glyph = translation
glyph = segments
stranded = 1
translation = 1frame
bgcolor = palegoldenrod
fgcolor = goldenrod
label = 1
key = CDS
citation = Protein coding sequence (CDS or translation; annotation DB ; Chado)
keygroup = " Genomic features"
#link = "#"
# [orthogene]
# feature = gene orthologous_region
# glyph = transcript2
# fgcolor = blue
# bgcolor = palegoldenrod
# secondary = gene
# secondary_bgcolor = palegoldenrod
# secondary_fgcolor = brown
# label = 1
# label density = 50
# height = 4
# key = Orthogene
# citation = Orthologous_region
# keygroup = " Synteny features"
# ## if use rename() need to use $f->id()? for link
# link = sub { my $f= shift; my $tp= $f->primary_tag;
# my ($id)= $f->each_tag_value('id');
# if ($tp eq 'gene') { return '/cgi-bin/fbidq.html?'.$id; }
# #my ($id)= $f->each_tag_value('id');
# unless ($id) { my $nm= $f->name(); $id= $nm if ($nm=~/^ortho:/); }
# if ($id) { return '?syn='.$id; }
# }
# rename = sub { my $f= shift; my $tn= '';
# my ($nt)= $f->each_tag_value('note');
# if ($nt =~ m/to_species=([^;,]+)/) { $tn .= ucfirst($1).'\\'; }
# if ($nt =~ m/to_name=([^;,]+)/) { $tn .= $1; }
# $tn ||= $f->info;
# return $tn;
# }
[orthologous_region]
feature = orthologous_region
glyph = transcript2
# glyph = segments
# no_arrows = 0
bgcolor = palegoldenrod
fgcolor = turquoise
label = 1
label density = 50
height = 4
key = Ortholog
citation = Orthologous_region
keygroup = " Synteny features"
link = sub { my $f= shift;
my ($nt)= $f->each_tag_value('note');
#to_name=CG31119-PA;to_species=dmel
if ($nt =~ m/to_name=[^; ]*((CG|CR|TE)\d+)/) {
return '/cgi-bin/fbidq.html?'.$1;
}
my ($id)= $f->each_tag_value('id');
unless ($id) { my $nm= $f->name(); $id= $nm if ($nm=~/^ortho:/); }
if ($id) { return '?syn='.$id; }
}
rename = sub { my $f= shift; my $tn= '';
my ($nt)= $f->each_tag_value('note');
if ($nt =~ m/to_name/){
if ($nt =~ m/to_species=([^;,]+)/) { $tn .= ucfirst($1).'\\'; }
if ($nt =~ m/to_name=([^;,]+)/) { my $n=$1; $n=~s/-\w\w//; $tn .= $n; }
}
$tn ||= $f->info; # == ortho:nnn, not wanted
return $tn;
}
title = sub { my $f= shift;
my $t= $f->class .":". $f->info;
my ($nt)= $f->each_tag_value('note');
if ($nt =~ m/to_name=[^; ]*((CG|CR|TE)\d+)/) {
my $oid=$1; $t .= " ".$oid unless($t=~/$oid/);
}
$t .= " ". $f->seq_id .':'.$f->start."..".$f->end;
return $t;
}
# title = sub { my $f= shift; my $tn= ''; my $nt;
# $nt= $f->each_tag_value('note'); ##$nt ||= $f->description;
# if ($nt =~ m/to_species=([^;,]+)/) { $tn .= $1.'\\'; }
# if ($nt =~ m/to_name=([^;,]+)/) { $tn .= $1; }
# $tn ||= $f->info;
# return $f->class .":". $tn . " ". $f->seq_id .':'.$f->start."..".$f->end;
# }
[syntenic_region]
feature = syntenic_region
glyph = segments
#glyph = transcript2
bgcolor = pink
fgcolor = darkred
label = 1
key = Syntenic region
citation = Syntenic_region
keygroup = " Synteny features"
link = sub { my $f= shift; if ($f->name()) { return '?syn='.$f->name(); } }
[gene_genscan]
feature = gene:genscan mRNA:genscan
glyph = transcript2
bgcolor = tan
fgcolor = brown
secondary = mRNA:genscan
secondary_bgcolor = lightslategray
label = 1
key = Gene (Genscan)
citation = Genscan predicted Gene and mRNA
keygroup = "Analysis features"
link = "#"
[gene_genewise]
feature = gene:genewise mRNA:genewise
glyph = transcript2
bgcolor = lightgreen
fgcolor = green
secondary = mRNA:genewise
secondary_bgcolor = lightslategray
label = 1
key = Gene (Genewise)
citation = Genewise predicted Gene and mRNA
keygroup = "Analysis features"
link = "#"
[gene_twinscan]
feature = gene:twinscan mRNA:twinscan
glyph = transcript2
bgcolor = yellow
fgcolor = orange
secondary = mRNA:twinscan
secondary_bgcolor = lightslategray
label = 1
key = Gene (Twinscan)
keygroup = "Analysis features"
citation = Twinscan predicted Gene and mRNA
link = "#"
[mb_nadbESTdpse]
feature = match:blastn:na_dbEST.dpse
glyph = segments
stranded = 1
bgcolor = lightslategray
fgcolor = black
key = Dpse dbEST
citation = match:blastn:na_dbEST.dpse
keygroup = "Analysis features"
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;
}
[m_blastz]
feature = match:blastz
glyph = segments
stranded = 1
bgcolor = lightslategray
fgcolor = black
key = match:blastz
citation = match:blastz
keygroup = "Analysis features"
link = "#"
NOTlink = sub { my $v=shift->name(); $v=~s/^(GB)[:]//; $v=~s/[:.].*$//;
return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$v;
}
[mt_Dmelr31]
feature = match:tblastn:Dmel_r3.1
glyph = segments
stranded = 1
bgcolor = lightslategray
fgcolor = black
key = Dmel r31 transcript
citation = match:tblastn:Dmel_r3.1
keygroup = "Analysis features"
link = sub { my $v=shift->name(); $v=~s/^(GB)[:]//; $v=~s/[:.].*$//;
return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$v;
}
[blast]
feature = blast
glyph = alignment
bgcolor = darkorchid
fgcolor = darkorchid
bump = 1
label = 1
key = Blast hit
height = 8
citation = BLAST alignment hit
keygroup = "hidden"
link = "#"
# [contig]
# feature = contig
# glyph = extending_arrow
# no_arrows = 1
# #west = 1
# base = 0
# bgcolor = lightslategray
# fgcolor = lightslategray
# linewidth = 2
# bump = 1
# label = 1
# key = Contig
# citation = Contig (annotation DB ; Chado)
# keygroup = " Genome reagents"
# # link = sub { my $f= shift;
# # return ($f->name())?'/cgi-bin/fbannq.html?DBX='.$f->name() : ''; }
## bad data in dpse chado db
#[NOTscaffold]
#feature = NOTscaffold
#glyph = anchored_arrow
#no_arrows = 1
#base = 0
#fgcolor = black
#bgcolor = black
#linewidth = 2
#bump = 1
#label = 1
#height = 4
#key = GenBank Scaffold
#citation = segment (annotation DB ; Chado)
#keygroup = " Genome reagents"
#link = sub { my $nm= shift->name(); return ($nm)?'/cgi-bin/fbannq.html?ARM='.$nm : ''; }