diff --git a/gdump b/gdump
new file mode 100755
index 000000000..067e2f359
--- /dev/null
+++ b/gdump
@@ -0,0 +1,422 @@
+#!/usr/bin/perl
+
+use strict;
+use lib '../../lib';
+use CGI::Carp qw/fatalsToBrowser/;
+use CGI qw/:standard :html3 escape *table *TR *td *pre/;
+use Bio::DB::GFF;
+use Bio::Graphics::FeatureFile;
+use constant CONFIG => '/home4/www/sumo/conf/gbrowse.conf/01.human.conf';
+
+my $data = Bio::Graphics::FeatureFile->new(-file=>CONFIG) or die "data $!";
+my @aggregators = split /\s+/,$data->setting(general => 'aggregators');
+my $seqfactory = Bio::DB::GFF->new(-adaptor => 'dbi::mysqlopt',
+ -user => 'nobody',
+ -pass => '',
+ -dsn => 'dbi:mysql:hg12:host=sumo',
+ -aggregators => \@aggregators,
+ );
+
+# Get info for the possible features
+my %fmethod = ();
+my @tracks = $data->configured_types;
+
+for my $track (@tracks) {
+ next unless $data->setting($track=>'feature') and
+ $data->setting($track=>'key');
+ my @low_level_features = split /\s+/,$data->setting($track=>'feature');
+ $fmethod{$data->setting($track=>'key')}=\@low_level_features;;
+}
+my @results;
+if(param()){
+ if(param('links') and !param('recurse')){
+
+ print header('text/html'),
+ '',"\n";
+ } elsif(!param('recurse')) { print header('text/plain'); }
+
+ @results = dumper($seqfactory, \%fmethod, param('recurse'));
+ exit unless param('recurse');
+}
+my $recurse = join "\n",@results;
+
+print header();
+print start_html(-style=>{-src=>'/style/default.css'});
+print h1("GDump");
+&print_HTML(\%fmethod);
+exit;
+
+########################### end of program #################################
+
+sub print_HTML {
+my $fmethod = shift;
+
+# HTML form
+print start_multipart_form,
+ table({-width=>'100%',-cellspacing=>'1', -cellpadding=>'5'},
+ TR({-class=>'searchtitle'},
+ th({-width=>'33%'},'1. Sequences to Search'),th({-width =>'33%'},'2. Features'),
+ th({-width =>'33%'},'3. Options')),
+ TR({-class=>'searchbody'},
+ td({-align=>'center'},
+ table({-align =>'center'},
+ TR(td({-align=>'LEFT'},
+ em('Either'),'choose a pre-defined search:')),
+ TR(td(scrolling_list(-name=>'prefab',
+ -size=>5,
+ -value=>["NONE",
+ "all chromosomes",
+ ],
+ -default=> "NONE",
+ ),)),
+ TR(td(br,
+ em('Or'),'type in a list of sequence or chromosome names:',
+ br,'e.g.',' ',
+ '"1',' ','X"')),
+ TR(td(textarea(-name=>'list',
+ -rows=>7,
+ -cols=>21,
+ -wrap=>'off',
+ -value=>$recurse,
+ -force=>1
+ ),)),
+ TR(td(
+ br,em('Or'),
+ 'upload a file with sequence or chromosome names:')),
+ TR(td(filefield(-size=>20,
+ -name=>'upload'
+ ),)),
+ ) #end mini table
+ ),
+
+ td({-align=>'center'},
+ scrolling_list(-name=>'feature',
+ -size=>21,
+ -multiple=>1,
+ -default => ['Gene Models'],
+ -values=>[sort (keys(%$fmethod))])
+ ),
+
+ td(
+ 'Dump As:',
+ radio_group(-name=>'dump',
+ -values=>['FastA','Flatfile'],
+ -default=>'FastA'),br,
+
+ 'Compare Features Using:',
+ radio_group(-name=>'logic',
+ -values=>['AND','OR','XOR','NOT'],
+ -default=>'OR'),br,
+
+ 'Coordinates Relative to:',
+ radio_group(-name=>'relative',
+ -values=>['Query','Chromosome'],
+ -default=>'Query'),br,
+
+ checkbox_group(-name=>'DNA',
+ -values=>['Show DNA'],
+ -default=>['Show DNA']),br
+
+ dd,textfield(-name=>'flank5',
+ -size=>4,
+ -maxlength=>4,
+ -default=>0),'bp 5\' flank',
+
+ dd,checkbox_group(-name=>'flanked',
+ -values=>['feature'],
+ -default=>['feature']),
+
+ dd,textfield(-name=>'flank3',
+ -size=>4,-maxlength=>4,
+ -default=>0),'bp 3\' flank',
+ br,
+
+ checkbox_group(-name=>'links',
+ -values=>['As HTML'],
+ -default=>['As HTML']),br,
+ checkbox_group(-name=>'verbose',
+ -values=>['Verbose'],
+ -default=>['Verbose']),br,
+
+ 'Match regex: ',textfield(-name=>'grep'),br,
+ checkbox_group(-name=>'recurse',
+ -values=>['Paste']),
+ 'results back into Sequences to Search box'
+ )
+ ),
+
+ TR({-class =>'searchtitle'},
+ td(reset()),
+ td({-align =>'CENTER',},submit("DUMP")),
+ td(" ")
+ ),
+
+ ),
+ endform;
+return (\%fmethod);
+}
+
+#******************************************************************************
+sub dumper {
+ my $seqfac = shift;
+ my $fmethod = shift;
+ my $return = shift;
+
+ my $match = 0;
+ my $logic = param('logic');
+ my @features = param('feature');
+
+ #hack for when 'AND' is selected, but there is only one feature selected
+ if(scalar(@features) == 1 && $logic eq 'AND'){param(-name=>'logic',-value=>'OR'); dumper($seqfactory); exit;}
+
+ my %features = map{$_=>1} @features;
+
+ #****************************************************************************
+ # Get items ......
+ my @items;
+ if (param('prefab') ne "NONE"){
+ my $items = parse_prefab(param('prefab')); @items = @$items;
+ } # => param prefab must be none
+
+ elsif (my $fh = param('upload')){ # Use uploaded file
+ while(<$fh>){
+ @items = split /\s+|\s*,\s*/s, $_; # split on white sp, or comma
+ }
+ if (!@items){
+ print h2("Error: File must contain sequences that are space or comma delimited.");
+ exit;
+ }
+ } # => param prefab is none, no file uploaded, => check list
+
+ elsif (param('list')) { # get info from list
+ @items = split /\s+/s, param('list');
+ }
+
+ if (!@items){
+ print h2("Error: no sequences selected! You must choose one of these:",
+ br," "x64,"a) select a pre-defined search",br,
+ " "x64,"b) type a list of sequences",br,
+ " "x64,"c) upload a file");
+ exit;
+ }
+
+ #****************************************************************************
+ my @returns;
+ foreach my $item (@items){
+ # foreach chosen seq, get the sequence from Bio::DB::GFF
+ my $segment;
+ my @prev_returns = @returns;
+ if($item =~ /(\w+):(\d+),(\d+)/){
+ ($segment) = $seqfac->segment($1 , $2 => $3);
+ } else {
+ ($segment) = $seqfac->segment($item);
+ }
+ if (!defined($segment))
+ {print h4("Error: No sequence found for \"$item\""); next;};
+
+ #**************************************************************************
+ if($logic eq 'OR' or $logic eq 'AND' or $logic eq 'XOR'){
+ foreach my $feature (@features){
+ my @get_features = @{$fmethod->{$feature}};
+ foreach my $get_feature (@get_features){
+ my $iterator = $segment->features(-type=>$get_feature,-iterator=>1);
+ while (my $i = $iterator->next_feature) {
+ if($logic eq 'OR'){
+ $match = (param('dump') eq 'FastA') ?
+ asFasta($segment,$i,$return) : asTabbed($segment,$i,$return);
+ push @returns, $match;
+ }
+ elsif($logic eq 'AND' or $logic eq 'XOR') {
+ my $fstring = join " ", $i->features();
+ my $show = 1;
+ my $xor = 0;
+# foreach(@get_features){
+ foreach(@features){
+ unless($fstring =~ m!$_!){$show = 0; $xor++;}
+ }
+ if($show and $logic eq 'AND'){
+ $match = (param('dump') eq 'FastA') ?
+ asFasta($segment,$i,$return) : asTabbed($segment,$i,$return);
+ push @returns, $match;
+ }
+ elsif( !$show and $logic eq 'XOR' and ($xor == $#get_features) ){
+ $match = (param('dump') eq 'FastA') ?
+ asFasta($segment,$i,$return) : asTabbed($segment,$i,$return);
+ push @returns, $match;
+ }
+ } # end elsif ($logiv AND or XOR
+ } # end while
+ } # end of get_features
+ } # end foreach $feature
+ } # end of if ($logic...)
+ elsif($logic eq 'NOT'){
+ my $iterator = $segment->features(-iterator=>1);
+ while (my $i = $iterator->next_feature) {
+ next if $features{$i->method};
+ $match = (param('dump') eq 'FastA') ? asFasta($segment,$i,$return)
+ : asTabbed($segment,$i,$return);
+ push @returns, $match;
+ }
+ }
+ print h4("No data for $item") if @prev_returns ==@returns;
+ } # end of foreach $item
+
+ #****************************************************************************
+ # If there are no hits....
+ if (!@returns){
+ my $print_features = join ", ", @features;
+ if ($print_features){
+ print h2("Results: No data for any features selected:",$print_features);
+ }
+ else {print h2("Error: no features selected!!");}
+ }
+ return @returns if $return;
+}# end sub
+
+
+###############################################################################
+sub parse_prefab{
+ my $prefab = shift;
+ my @items;
+ if ($prefab eq 'all chromosomes'){
+ @items = qw(1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y);
+ }
+ elsif ($prefab eq "all genes") {
+# @items = $DB->fetch(-query=>'find predicted_gene');
+ }
+ else { # for all confirmed genes and all genet. def. genes
+# @items = $prefab eq "all confirmed genes"? $DB->fetch('Gene'=>'*')
+# :$DB->fetch(-query=>'find Sequence Confirmed_by');
+ }
+ return \@items;
+} # end parse prefab
+
+
+###############################################################################
+sub asFasta {
+ my ($segment,$feature,$return) = @_;
+ $segment->absolute(1) if param('relative') eq 'Chromosome';
+ $feature->absolute(1) if ((param('relative') eq 'Chromosome') or $return);
+
+ my $grep = param('grep') or undef;
+ my $dna = param('DNA')
+ ? get_dna($segment,$feature)."\n"
+ : undef;
+ my $verbose = param('verbose')? $feature->type : undef;
+ my $query = $segment->refseq.':'.$feature->start.','.$feature->stop;
+ my $label = $feature;
+# my $label = param('links') ? a({-href=>Object2URL($feature->group->name,$feature->group->class)},$feature)
+# : $feature;
+
+ my $header = join ' ',(">$query",$label,$verbose,"\n");
+ if($grep and param('links')){
+ markup(\$dna,$grep,'SPAN','match');
+ }
+
+ if($header.$dna =~ /($grep)/gs){
+ next unless $1 eq $grep; #comes out as '/' sometimes... why?
+ if($return){
+ return $query;
+ }
+ #this step is SLOW
+ justify(\$dna,80);
+ print $header.$dna and return $feature;
+ }
+ return undef;
+}# end sub fasta
+
+###############################################################################
+sub asTabbed {
+ my ($segment,$feature,$return) = @_;
+ $segment->absolute(1) if param('relative') eq 'Chromosome';
+ $feature->absolute(1) if ((param('relative') eq 'Chromosome') or $return);
+
+ my $grep = param('grep') or undef;
+ my $dna = param('DNA')
+ ? get_dna($segment,$feature)
+ : undef;
+ my $verbose = param('verbose')? "\t" . $feature->type : undef;
+ my $query = $segment->refseq.':'.$feature->start.','.$feature->stop;
+# my $label = param('links') ? a({-href=>Object2URL($feature->group->name,$feature->group->class)},$feature) : $feature;
+ my $label = $feature;
+
+ if($grep and param('links')){
+ markup(\$dna,$grep,'SPAN','match');
+ }
+ my $outstr = join "\t",($query,$label,$verbose,$dna),"\n";
+
+ if($outstr =~ /$grep/gs){
+ return $query if $return;
+ return undef if $return;
+ print $outstr and return $feature;
+ }
+} # end of sub asTabbed
+
+###############################################################################
+sub justify {
+ my $dna = shift;
+ my $col = shift;
+
+#print b($$dna);
+
+ my ($jdna,$count,$inside);
+ for my $i(0..length($$dna)){
+
+ $inside = 1 if(substr($$dna,$i,1) eq '<');
+ $inside = 0 if(substr($$dna,$i-1,1) eq '>');
+ $count++ unless $inside;
+
+ $jdna .= substr($$dna,$i,1);
+ $jdna .= "\n" unless ($count % $col or $inside);
+ }
+ $$dna = $jdna;
+} # end of sub justify
+
+###############################################################################
+sub markup {
+ my $tmpstr = '---chopped---';
+ my ($subject,$grep,$tag,$class) = @_;
+ my $c = $class ? " CLASS=\"$class\"" : undef;
+ my ($head,$tail) = ("<$tag$c>","");
+
+ return undef unless $$subject;
+ return undef unless $$subject =~ m!$grep!s;
+
+ #FIND THEM ALL !!!!!!!!!!
+ my @greppeds = ();
+ while($$subject =~ s!($grep)!$tmpstr!s){push @greppeds,$1;};
+
+ #extract tags;
+ my @postpends;
+ foreach my $grepped (@greppeds){
+ my $postpend = undef;
+ while($grepped =~ s!(<.+?>)!!s){my $t = $1; $postpend .= $t;}
+ push @postpends, $postpend;
+ }
+
+ foreach my $g (@greppeds){
+ my $p = shift @postpends;
+ $$subject =~ s!(.*?)$tmpstr!$1$head$g$tail$p!s;
+ }
+ return 1;
+}# end of sub markup
+
+###############################################################################
+sub get_dna {
+ my($segment,$feature) = @_;
+ my $flank5 = param('flank5') or 0;
+ my $flank3 = param('flank3') or 0;
+
+ $flank5 -- if $flank5 > 0;
+ $flank3 -- if $flank3 > 0;
+
+ my $dna5 =$segment->subseq(($feature->start - $flank5),
+ $feature->start)->dna if $flank5;
+ $dna5 = ''.$dna5.'' if param('links') and $dna5;
+ my $dna3 = $segment->subseq($feature->stop,
+ ($feature->stop + $flank3))->dna if $flank3;
+ $dna3 = ''.$dna3.'' if param('links') and $dna3;
+ my $dnaed = param('flanked') ? $feature->dna : '-';
+
+ return $dna5.$dnaed.$dna3;
+}# end of sub get dna