# 07.dmel41my.conf
# gbrowse config file for gff mysql-indexed gene features
# d.gilbert, may05
#slight modifications by Scott Cain to include with GBrowse dist
# should work well with current flybase GFF3
[GENERAL]
description = D. melanogaster (dmelr41; MySQL)
header = <h2><i>D. melanogaster</i> Genome,
<small>Annotation Release 4.1; Feb 2005
using MySQL-GFF data adaptor
</small> </h2>
adaptor = dbi::mysql
database = dbi:mysql:database=flybase
user = nobody
passwd =
aggregators = transcript alignment
default name = 4:100000-200000
# examples to show in the introduction
examples =
X 2L 2R 3L 3R 4
chromosome_arm:4
2L:80,000..120,000
4:200000..500000
plex* Ank
Gadfly:CG11186 FlyBase:FBan0011186
plugins = BatchDumper FastaDumper GFFDumper
cache_overview = 360
cachedir = 360
# Web site configuration info
stylesheet = /gbrowse/gbrowse.css
buttons = /gbrowse/images/buttons
tmpimages = /gbrowse/tmp
help = /gbrowse/
# Default glyph settings
glyph = generic
height = 8
bgcolor = cyan
fgcolor = cyan
label density = 25
bump density = 100
# where to link to when user clicks in detaild view
# NOTlink =AUTO
# generic FB link - should work if FB id is in data
link = sub {
my $f= shift;
my $d= join(',',$f->each_tag_value('ID'),$f->id(),$f->each_tag_value('Dbxref'));
my $tp= $f->class;
my $best='(FB\w\w\d+)';
if($tp =~ /gene/i) { $best='(FBgn\d+)'; } # FBgn or FBan?
elsif($tp =~ /MRNA|CDS/i) { $best='(C[GR]\d+)'; }
elsif($tp =~ /intron|UTR/i) { $best='(C[GR]\d+)'; }
elsif($tp =~ /transposable_element/i) { $best='(FBti\d+)'; }
elsif($tp =~ /cyto/i) { $best='(FB(ab|ba)\d+)'; }
if ($d =~ /$best/){ return 'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
elsif ($d =~ /(FB\w\w\d+)/){ return 'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
elsif ($d =~ /((C[GR]|TE)\d+)/ ){ return 'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
if ($f->name()) { return 'http://flybase.org/cgi-bin/fbsymq.html?'.$f->name(); }
}
title = sub { my $f= shift;
return $f->method .":". $f->info . " ". $f->seq_id .':'.$f->start."..".$f->end;
}
## suggested display name change ? is this active
## this works .. but cant do at general level here; needs to be in each feature def
label = sub { my $f = shift;
my @n = ($f->attributes('Name'), $f->attributes('Alias'));
return $n[0] || $f->display_name;
}
# what image widths to offer
image widths = 450 640 800 1024
# default width of detailed view (pixels)
default width = 800
default features = gene scaffold
# max and default segment sizes for detailed view
max segment = 1000001
default segment = 100000
# low-res boundary
low res = 200000
# zoom levels
zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000
# colors of the overview, detailed map and key
overview units = M
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Gene Symbol
language = en
# a footer
footer = <hr>
<table width="100%">
<TR>
<TD align="LEFT" class="databody">
For the source code for this browser, see the <a href="http://www.gmod.org">
Generic Model Organism Database Project.</a> For other questions, send
mail to <a href="mailto:lstein@cshl.org">lstein@cshl.org</a>.
</TD>
</TR>
</table>
<hr>
<pre>$Id: 03.fly.conf,v 1.3 2005-12-09 22:19:09 mwz444 Exp $</pre>
# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 =
html4 =
html5 =
html6 =
### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks
[gene]
feature = gene transcript
glyph = transcript2
bgcolor = lightblue
fgcolor = blue
secondary = mRNA
secondary_bgcolor = mediumblue
secondary_fgcolor = mediumblue
highlight_color = red
higlighted = 1
label = sub { my $f = shift;
my @n = ($f->attributes('Name'), $f->attributes('Alias'));
return $n[0] || $f->display_name;
}
label density = 50
bump density = 150
key = Gene Model
category = ' Genomic features'
citation = Gene and mRNA (transcript) features (annotation DB ; Chado)
[genespan]
feature = gene
glyph = segments
stranded = 1
bgcolor = lightblue
fgcolor = blue
highlight_color = red
higlighted = 1
label = sub { my $f = shift;
my @n = ($f->attributes('Name'), $f->attributes('Alias'));
return $n[0] || $f->display_name;
}
label density = 50
bump density = 150
key = Gene span
category = ' Gene Model subfeatures'
citation = Gene span features (annotation DB ; Chado)
# an aggregator feature
[mRNA]
feature = transcript
glyph = segments
stranded = 1
translation = 1frame
bgcolor = palegoldenrod
fgcolor = goldenrod
label = sub { my $f = shift;
my @n = ($f->attributes('Name'), $f->attributes('Alias'));
return $n[0] || $f->display_name;
}
key = mRNA
citation = Transcript (mRNA; annotation DB ; Chado)
category = ' Gene Model subfeatures'
[CDS]
feature = CDS
glyph = segments
stranded = 1
translation = 1frame
bgcolor = palegoldenrod
fgcolor = goldenrod
#label = 1
label = sub { my $f = shift;
my @n = ($f->attributes('Name'), $f->attributes('Alias'));
return $n[0] || $f->display_name;
}
key = CDS
citation = Protein coding sequence (CDS or translation; annotation DB ; Chado)
category = ' Gene Model subfeatures'
[intron]
feature = intron
glyph = segments
stranded = 1
label = sub { my $f = shift;
my @n = ($f->attributes('Name'), $f->attributes('Alias'));
return $n[0] || $f->display_name;
}
key = intron
citation = intron
category = ' Gene Model subfeatures'
link = "#"
[five_prime_UTR]
feature = five_prime_UTR
glyph = segments
stranded = 1
label = sub { my $f = shift;
my @n = ($f->attributes('Name'), $f->attributes('Alias'));
return $n[0] || $f->display_name;
}
key = 5prime UTR
citation = five_prime_UTR
category = ' Gene Model subfeatures'
link = "#"
[three_prime_UTR]
feature = three_prime_UTR
glyph = segments
stranded = 1
label = sub { my $f = shift;
my @n = ($f->attributes('Name'), $f->attributes('Alias'));
return $n[0] || $f->display_name;
}
key = 3prime UTR
citation = three_prime_UTR
category = ' Gene Model subfeatures'
link = "#"
#---------------------------------
[pseudogene]
feature = pseudogene
glyph = segments
strand_arrow = 1
fgcolor = orange
label = sub { my $f = shift;
my @n = ($f->attributes('Name'), $f->attributes('Alias'));
return $n[0] || $f->display_name;
}
key = Pseudogene
category = ' Genomic features'
[tRNA]
feature = tRNA
bgcolor = white
fgcolor = black
curatedexon = slateblue
fontcolor = slateblue
height = 3
key = tRNAs
category = ' Genomic features'
[noncodingRNA]
feature = ncRNA snoRNA snRNA miscRNA
glyph = generic
bgcolor = peachpuff
height = 4
stranded = 1
key = Various non coding RNAs
category = ' Genomic features'
[transposable]
feature = transposable_element
bgcolor = magenta
fgcolor = magenta
label = sub { my $f = shift;
my @n = ($f->attributes('Name'), $f->attributes('Alias'));
return $n[0] || $f->display_name;
}
glyph = anchored_arrow
key = Natural transposon
citation = Natural transposon (annotation DB ; Chado)
category = ' Genomic features'
[tinsert]
feature = transposable_element_insertion_site
glyph = pinsertion
bgcolor = darkturquoise
fgcolor = darkturquoise
bump = 1
label = 0
key = Transgene insertion site
citation = Transgene insertion site (annotation DB ; Chado)
category = ' Genomic features'
link = sub {
my $f= shift; my($d);
$d= join(',',$f->each_tag_value('ID'),$f->each_tag_value('Dbxref'),$f->primary_id());
if ($d =~ /(FBti\d+)/||$d =~ /((FB\w\w|TE)\d+)/) { return 'http://flybase.org/cgi-bin/fbidq.html?'.$1; }
if ($f->name()) { return 'http://flybase.org/cgi-bin/fbinsq.html?symbol='.$f->name(); }
}
#-------- Misc. Genomic features -------------------
[polyA_site]
feature = polyA_site
#glyph = segments
strand_arrow = 1
bgcolor = lightslategray
fgcolor = lightslategray
key = polyA_site
citation = polyA_site (annotation DB ; Chado)
category = ' Misc. Genomic features'
link = sub {
my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v;
}
# Gsc-polyA_site-585205..585205 2L
[point_mutation]
feature = point_mutation
# glyph = segments
bgcolor = lightslategray
fgcolor = lightslategray
key = point_mutation
citation = point_mutation (annotation DB ; Chado)
category = ' Misc. Genomic features'
link = sub {
my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v;
}
[protein_binding_site]
feature = protein_binding_site
# glyph = segments
strand_arrow = 1
bgcolor = lightslategray
fgcolor = lightslategray
key = protein_binding_site
citation = protein_binding_site (annotation DB ; Chado)
category = ' Misc. Genomic features'
link = sub {
my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v;
}
[rescue_fragment]
feature = rescue_fragment
# glyph = segments
strand_arrow = 1
bgcolor = lightslategray
fgcolor = lightslategray
key = rescue_fragment
citation = rescue_fragment (annotation DB ; Chado)
category = ' Misc. Genomic features'
link = sub {
my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v;
}
[mature_peptide]
feature = mature_peptide
glyph = segments
strand_arrow = 1
bgcolor = palegoldenrod
fgcolor = orange
key = mature_peptide
citation = mature_peptide (annotation DB ; Chado)
category = ' Misc. Genomic features'
link = sub {
my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v;
}
[enhancer]
feature = enhancer
# glyph = segments
strand_arrow = 1
bgcolor = lightslategray
fgcolor = lightslategray
key = enhancer
citation = enhancer (annotation DB ; Chado)
category = ' Misc. Genomic features'
link = sub {
my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v;
}
[aberration_junction]
feature = aberration_junction
# glyph = segments
strand_arrow = 1
bgcolor = lightslategray
fgcolor = lightslategray
key = aberration_junction
citation = aberration_junction (annotation DB ; Chado)
category = ' Misc. Genomic features'
link = sub {
my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v;
}
# add: regulatory_region and sequence_variant
[regulatory_region]
feature = regulatory_region
# glyph = segments
strand_arrow = 1
bgcolor = lightslategray
fgcolor = lightslategray
key = regulatory_region
citation = regulatory_region (annotation DB ; Chado)
category = ' Misc. Genomic features'
link = sub {
my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v;
}
[sequence_variant]
feature = sequence_variant
# glyph = segments
strand_arrow = 1
bgcolor = lightslategray
fgcolor = lightslategray
key = sequence_variant
citation = sequence_variant (annotation DB ; Chado)
category = ' Misc. Genomic features'
link = sub {
my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return 'http://flybase.org/cgi-bin/fbannq.html?synonym='.$v;
}
[DNA_motif]
feature = DNA_motif RNA_motif
# glyph = segments
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 (annotation DB ; Chado)
category = ' Misc. Genomic features'
link = "#"
[chromosome_band]
feature = chromosome_band
glyph = generic
bgcolor = blue
fgcolor = blue
height = 4
key = chromosome_band
##category = ' Misc. Genomic features'
#---------- Small Genome reagents --------------
[DGC]
feature = match:sim4:na_DGC_dros
glyph = segments
strand_arrow = 1
label = sub { my $f = shift;
my @n = ($f->attributes('Name'), $f->attributes('Alias'));
return $n[0] || $f->display_name;
}
bgcolor = plum
fgcolor = black
key = DGC EST/cDNA
citation = DGC cDNA_clone (annotation DB ; Chado)
category = ' Genome reagents'
link = sub {
my $f= shift;
my $v= $f->name(); my @v= $f->each_tag_value('Name');
$v= shift @v if (@v>0);
$v=~s/[:.].*(prime|contig).*$//; $v=~s/^(GB)[:]//;
return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$v;
}
[EST]
feature = match:sim4:na_dbEST.same.dmel match:sim4:na_dbEST.diff.dmel
glyph = segments
strand_arrow = 1
bgcolor = lightgreen
fgcolor = green
key = EST
citation = EST (annotation DB ; Chado)
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;
}
#drop from link name: .5prime_revcomp .5prime, :contig1, SD02026:contig1, CK02552.5prime
# but for ones like GB:AV399447 drop db:
[oligo]
feature = oligo
glyph = generic
bgcolor = tomato
fgcolor = tomato
height = 4
bump = 0
bump density = 1
label = 0
label density = 0
key = Affy Oligo
citation = oligonucleotide (annotation DB ; Chado)
category = ' Genome reagents'
link = sub { my $f= shift;
return ($f->name())?'http://flybase.org/cgi-bin/fbannq.html?oligo='.$f->name() : ''; }
#-------- Analysis -------------------
# from match:promoter ?
[transcription_start_site]
feature = transcription_start_site
glyph = generic
bgcolor = purple
fgcolor = purple
bump = 1
label = 0
label density = 0
key = Promoter prediction
citation = Transcription promoter prediction (annotation DB ; Chado)
category = ' Analysis features'
link = "#"
[repeat_region]
feature = repeat_region match:repeat_runner_seg match:repeatmasker
# glyph = extending_arrow
bgcolor = darkorchid
fgcolor = darkorchid
height = 3
connector = solid
bump = 1
strand_arrow = 0
label = 0
label density = 0
key = Repeat region
citation = repeat_region (annotation DB ; Chado)
category = ' Analysis features'
link = "#"
[mRNA_genscan]
feature = mRNA_genscan match:genscan
glyph = segments
strand_arrow = 1
bgcolor = tan
fgcolor = brown
connector = solid
bump = 1
label = sub { my $f = shift;
my @n = ($f->attributes('Name'), $f->attributes('Alias'));
return $n[0] || $f->display_name;
}
key = Genscan prediction
citation = Genscan (gene prediction) (annotation DB ; Chado)
category = ' Analysis features'
link = "#"
[mRNA_genie]
feature = mRNA_piecegenie match:genie
glyph = segments
strand_arrow = 1
bgcolor = yellow
fgcolor = brown
connector = solid
bump = 1
label = 0
label density = 0
key = Genie prediction
citation = PieceGenie (gene prediction) (annotation DB ; Chado)
category = ' Analysis features'
link = "#"
[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 (annotation DB ; Chado)
category = ' Analysis features'
link = "#"
[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 (annotation DB ; Chado)
category = ' Analysis features'
link = "#"
[tRNA_trnascan]
feature = tRNA:trnascan
glyph = transcript2
bgcolor = yellow
fgcolor = brown
connector = solid
bump = 1
label = 0
key = tRNAscan prediction
citation = tRNAscan (tRNA prediction) (annotation DB ; Chado)
category = ' Analysis features'
link = "#"
#-- BLAST features; combined some
[mb_aa_SPTR.dmel]
feature = match:blastx:aa_SPTR.dmel
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = D melanogaster protein
citation = match:blastx:aa_SPTR.dmel
category = ' Blast features'
link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//;
if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
}
[mx_nadpse]
feature = match:tblastx:na_dpse
glyph = segments
bgcolor = lightslategray
fgcolor = black
label = 1
link = AUTO
#sub {my $v=shift->name(); $v=~s/\-\d+.*$//; return '?source=dpse_overview&id='.$v if($v); }
key = D pseudoobscura contigs
citation = match:tblastx:na_dpse
category = ' Blast features'
[mb_na_agambiae]
feature = match:tblastx:na_agambiae
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Mosquito NA
citation = match:tblastx:na_agambiae
category = ' Blast 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;
}
[mb_aa_SPTR.insect]
feature = match:blastx:aa_SPTR.insect
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Insect protein
citation = match:blastx:aa_SPTR.insect
category = ' Blast features'
link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//;
if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
}
[mb_na_dbEST.insect]
feature = match:tblastx:na_dbEST.insect
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Insect dbEST
citation = match:tblastx:na_dbEST.insect
category = ' Blast 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;
}
[mb_aa_SPTR.worm]
feature = match:blastx:aa_SPTR.worm
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Worm protein
citation = match:blastx:aa_SPTR.worm
category = ' Blast features'
link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//;
if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
}
[mb_aa_SPTR.yeast]
feature = match:blastx:aa_SPTR.yeast
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Yeast protein
citation = match:blastx:aa_SPTR.yeast
category = ' Blast features'
link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//;
if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
}
[mb_aa_SPTR.othinv]
feature = match:blastx:aa_SPTR.othinv
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Other invert. protein
citation = match:blastx:aa_SPTR.othinv
category = ' Blast features'
link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//;
if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
}
[mb_aa_SPTR.primate]
feature = match:blastx:aa_SPTR.primate
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Primate protein
citation = match:blastx:aa_SPTR.primate
category = ' Blast features'
link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//;
if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
}
[mb_vert]
feature = match:blastx:aa_SPTR.rodent match:blastx:aa_SPTR.othvert
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Vertebrate protein
citation = Blastx rodent, vertebrate aa_SPTR
category = ' Blast features'
link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//;
if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
}
[mb_aa_SPTR.plant]
feature = match:blastx:aa_SPTR.plant
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Plant protein
citation = match:blastx:aa_SPTR.plant
category = ' Blast features'
link = sub { my $ac=shift->name(); $ac=~s/[:.].*$//;
if ($ac=~/^(L|N|M|P|Q|O|R|S|T|U|V|W)/) { return 'http://www.uniprot.org/entry/'.$ac; }
elsif ($ac) { return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Protein&doptcmdl=GenPept&tool=FlyBase&term='.$ac; }
}
#--- sim4 features
[ms_na_gb.dmel]
feature = match:sim4:na_gb.dmel
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Dmel genbank
citation = match:sim4:na_gb.dmel
category = ' Sim4 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;
}
[mst_na_gb.dmel]
feature = match:sim4tandem:na_gb.dmel
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Dmel genbank (sim4tandem)
citation = match:sim4tandem:na_gb.dmel
category = ' Sim4 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;
}
[ms_na_gb.tpa.dmel]
feature = match:sim4:na_gb.tpa.dmel
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Dmel genbank tpa
citation = match:sim4:na_gb.tpa.dmel
category = ' Sim4 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;
}
[ms_na_transcript_dmel_r32]
feature = match:sim4:na_transcript_dmel_r32
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Dmel r32 transcript
citation = match:sim4:na_transcript_dmel_r32
category = ' Sim4 features'
link = "#"
[ms_na_transcript_dmel_r31]
feature = match:sim4:na_transcript_dmel_r31
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Dmel r31 transcript
citation = match:sim4:na_transcript_dmel_r31
category = ' Sim4 features'
link = "#"
[ms_na_gadfly_dmel_r2]
feature = match:sim4:na_gadfly_dmel_r2
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Dmel r2 transcript
citation = match:sim4:na_gadfly_dmel_r2
category = ' Sim4 features'
link = "#"
[ms_na_smallRNA.dros]
feature = match:sim4:na_smallRNA.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Dros smallRNA
citation = match:sim4:na_smallRNA.dros
category = ' Sim4 features'
link = "#"
[ms_na_ARGs.dros]
feature = match:sim4:na_ARGs.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Dmel ARGs
citation = match:sim4:na_ARGs.dros
category = ' Sim4 features'
link = "#"
[ms_na_ARGsCDS.dros]
feature = match:sim4:na_ARGsCDS.dros
glyph = segments
bgcolor = lightslategray
fgcolor = black
key = Dmel ARGs CDS
citation = match:sim4:na_ARGsCDS.dros
category = ' Sim4 features'
link = "#"
#-------- Genome reagents -------------------
# see dgc,est above
# keep here so shows at top near BAC track
[blast]
feature = blast
glyph = alignment
bgcolor = darkorchid
fgcolor = darkorchid
bump = 1
label = 1
key = Blast hit
height = 8
citation = BLAST alignment hit
#category = 'hidden'
#hidden = 1
link = "#"
[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 (annotation DB ; Chado)
category = ' Genome reagents'
link = sub { my $nm= shift->name(); return ($nm)?'http://flybase.org/cgi-bin/fbannq.html?DBX='.$nm : ''; }
## aug04 - was segment; renamed to SO equivalent golden_path ???
[scaffold]
feature = scaffold
glyph = anchored_arrow
no_arrows = 1
base = 0
fgcolor = black
bgcolor = black
linewidth = 2
bump = 1
label = 1
height = 4
key = GenBank Scaffold
citation = golden_path segment (annotation DB ; Chado)
category = ' Genome reagents'
link = sub { my $nm= shift->name(); return ($nm)?'http://flybase.org/cgi-bin/fbannq.html?ARM='.$nm : ''; }
### feature count table: update w/ fsource grouping
# mysql> select count(f.fid),ft.ftypeid,ft.fmethod,ft.fsource
# -> from fdata f,ftype ft where f.ftypeid = ft.ftypeid
# -> group by ft.fmethod, ft.fsource;
#
#
# +--------------+---------+-------------------------------------+-----------------------------+
# | count(f.fid) | ftypeid | fmethod | fsource |
# +--------------+---------+-------------------------------------+-----------------------------+
# | 79 | 70 | aberration_junction | . |
# | 674 | 57 | BAC | . |
# | 18941 | 31 | CDS | . |
# | 6 | 2 | chromosome | . |
# | 6 | 7 | chromosome_arm | . |
# | 5770 | 3 | chromosome_band | . |
# | 6 | 1 | Component | reference |
# | 5 | 96 | DNA_motif | . |
# | 27 | 84 | enhancer | . |
# | 93075 | 12 | exon | . |
# | 21634 | 11 | five_prime_UTR | . |
# | 14066 | 20 | gene | . |
# | 408 | 63 | insertion_site | . |
# | 73345 | 34 | intron | . |
# | 434 | 5 | match | assembly:path |
# | 207911 | 30 | match | blastx:aa_SPTR.dmel |
# | 16610 | 51 | match | blastx:aa_SPTR.insect |
# | 21451 | 35 | match | blastx:aa_SPTR.othinv |
# | 18036 | 37 | match | blastx:aa_SPTR.othvert |
# | 11997 | 47 | match | blastx:aa_SPTR.plant |
# | 20850 | 33 | match | blastx:aa_SPTR.primate |
# | 21644 | 45 | match | blastx:aa_SPTR.rodent |
# | 13765 | 41 | match | blastx:aa_SPTR.worm |
# | 5593 | 39 | match | blastx:aa_SPTR.yeast |
# | 11063 | 94 | match | genie |
# | 17811 | 28 | match | genscan |
# | 139 | 99 | match | HDP |
# | 11758 | 58 | match | repeatmasker |
# | 110 | 78 | match | RNAiHDP |
# | 1062 | 65 | match | sim4:na_ARGs.dros |
# | 984 | 66 | match | sim4:na_ARGsCDS.dros |
# | 85910 | 25 | match | sim4:na_dbEST.diff.dmel |
# | 169078 | 14 | match | sim4:na_dbEST.same.dmel |
# | 6458 | 13 | match | sim4:na_DGC_dros |
# | 14249 | 22 | match | sim4:na_gadfly_dmel_r2 |
# | 26531 | 8 | match | sim4:na_gb.dmel |
# | 2214 | 68 | match | sim4:na_gb.tpa.dmel |
# | 98 | 75 | match | sim4:na_smallRNA.dros |
# | 19001 | 23 | match | sim4:na_transcript_dmel_r31 |
# | 18799 | 24 | match | sim4:na_transcript_dmel_r32 |
# | 23748 | 93 | match | sim4tandem:na_gb.dmel |
# | 101190 | 49 | match | tblastx:na_agambiae |
# | 34107 | 53 | match | tblastx:na_dbEST.insect |
# | 263465 | 43 | match | tblastx:na_dpse |
# | 295 | 81 | match:tRNAscan-SE | . |
# | 434 | 6 | match_part | assembly:path |
# | 364002 | 29 | match_part | blastx:aa_SPTR.dmel |
# | 37018 | 52 | match_part | blastx:aa_SPTR.insect |
# | 52260 | 36 | match_part | blastx:aa_SPTR.othinv |
# | 40052 | 38 | match_part | blastx:aa_SPTR.othvert |
# | 24905 | 48 | match_part | blastx:aa_SPTR.plant |
# | 52032 | 32 | match_part | blastx:aa_SPTR.primate |
# | 53213 | 46 | match_part | blastx:aa_SPTR.rodent |
# | 32318 | 42 | match_part | blastx:aa_SPTR.worm |
# | 11381 | 40 | match_part | blastx:aa_SPTR.yeast |
# | 41282 | 95 | match_part | genie |
# | 72887 | 27 | match_part | genscan |
# | 164 | 100 | match_part | HDP |
# | 11758 | 59 | match_part | repeatmasker |
# | 9198 | 91 | match_part | repeat_runner_seg |
# | 294 | 79 | match_part | RNAiHDP |
# | 5621 | 64 | match_part | sim4:na_ARGs.dros |
# | 4720 | 67 | match_part | sim4:na_ARGsCDS.dros |
# | 158509 | 26 | match_part | sim4:na_dbEST.diff.dmel |
# | 347084 | 16 | match_part | sim4:na_dbEST.same.dmel |
# | 10821 | 15 | match_part | sim4:na_DGC_dros |
# | 57603 | 17 | match_part | sim4:na_gadfly_dmel_r2 |
# | 78406 | 9 | match_part | sim4:na_gb.dmel |
# | 2260 | 69 | match_part | sim4:na_gb.tpa.dmel |
# | 124 | 76 | match_part | sim4:na_smallRNA.dros |
# | 86217 | 18 | match_part | sim4:na_transcript_dmel_r31 |
# | 89670 | 19 | match_part | sim4:na_transcript_dmel_r32 |
# | 68525 | 92 | match_part | sim4tandem:na_gb.dmel |
# | 101190 | 50 | match_part | tblastx:na_agambiae |
# | 51275 | 54 | match_part | tblastx:na_dbEST.insect |
# | 263465 | 44 | match_part | tblastx:na_dpse |
# | 295 | 82 | match_part:tRNAscan-SE | . |
# | 8 | 74 | mature_peptide | . |
# | 16884 | 21 | mRNA | . |
# | 140 | 87 | ncRNA | . |
# | 197525 | 55 | oligo | . |
# | 458 | 71 | point_mutation | . |
# | 123 | 73 | polyA_site | . |
# | 92 | 85 | protein_binding_site | . |
# | 39 | 80 | pseudogene | . |
# | 30 | 86 | region | . |
# | 137 | 88 | regulatory_region | . |
# | 9199 | 90 | repeat_region | . |
# | 135 | 62 | rescue_fragment | . |
# | 96 | 98 | rRNA | . |
# | 437 | 4 | scaffold | . |
# | 209 | 72 | sequence_variant | . |
# | 1 | 97 | signal_peptide | . |
# | 28 | 89 | snoRNA | . |
# | 29 | 77 | snRNA | . |
# | 16020 | 56 | three_prime_UTR | . |
# | 36921 | 10 | transcription_start_site | . |
# | 1571 | 61 | transposable_element | . |
# | 16404 | 60 | transposable_element_insertion_site | . |
# | 295 | 83 | tRNA | . |
# +--------------+---------+-------------------------------------+-----------------------------+
# 100 rows in set (7 min 6.01 sec)