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added changes to sims display
package Observation;
use lib '/vol/ontologies';
use DBMaster;
require Exporter;
@EXPORT_OK = qw(get_objects);
use FIG_Config;
#use strict;
#use warnings;
use HTML;
1;
# $Id: Observation.pm,v 1.32 2007/08/21 22:45:54 arodri7 Exp $
=head1 NAME
Observation -- A presentation layer for observations in SEED.
=head1 DESCRIPTION
The SEED environment contains various sources of information for sequence features. The purpose of this library is to provide a
single interface to this data.
The data can be used to display information for a given sequence feature (protein or other, but primarily information is computed for proteins).
=cut
=head1 BACKGROUND
=head2 Data incorporated in the Observations
As the goal of this library is to provide an integrated view, we combine diverse sources of evidence.
=head3 SEED core evidence
The core SEED data structures provided by FIG.pm. These are Similarities, BBHs and PCHs.
=head3 Attribute based Evidence
We use the SEED attribute infrastructure to store information computed by a variety of computational procedures.
These are e.g. InterPro hits via InterProScan (ipr), NCBI Conserved Domain Database Hits via PSSM(cdd),
PFAM hits via HMM(pfam), SignalP results(signalp), and various others.
=head1 METHODS
The public methods this package provides are listed below:
=head3 context()
Returns close or diverse for purposes of displaying genomic context
=cut
sub context {
my ($self) = @_;
return $self->{context};
}
=head3 rows()
each row in a displayed table
=cut
sub rows {
my ($self) = @_;
return $self->{rows};
}
=head3 acc()
A valid accession or remote ID (in the style of a db_xref) or a valid local ID (FID) in case this is supported.
=cut
sub acc {
my ($self) = @_;
return $self->{acc};
}
=head3 class()
The class of evidence (required). This is usually simply the name of the tool or the name of the SEED data structure.
B<Please note> the connection of class and display_method and URL.
Current valid classes are:
=over 9
=item IDENTICAL (seq)
=item SIM (seq)
=item BBH (seq)
=item PCH (fc)
=item FIGFAM (seq)
=item IPR (dom)
=item CDD (dom)
=item PFAM (dom)
=item SIGNALP_CELLO_TMPRED (loc)
=item PDB (seq)
=item TMHMM (loc)
=item HMMTOP (loc)
=back
=cut
sub class {
my ($self) = @_;
return $self->{class};
}
=head3 type()
The type of evidence (required).
Where type is one of the following:
=over 8
=item seq=Sequence similarity
=item dom=domain based match
=item loc=Localization of the feature
=item fc=Functional coupling.
=back
=cut
sub type {
my ($self) = @_;
return $self->{type};
}
=head3 start()
Start of hit in query sequence.
=cut
sub start {
my ($self) = @_;
return $self->{start};
}
=head3 end()
End of the hit in query sequence.
=cut
sub stop {
my ($self) = @_;
return $self->{stop};
}
=head3 start()
Start of hit in query sequence.
=cut
sub qstart {
my ($self) = @_;
return $self->{qstart};
}
=head3 qstop()
End of the hit in query sequence.
=cut
sub qstop {
my ($self) = @_;
return $self->{qstop};
}
=head3 hstart()
Start of hit in hit sequence.
=cut
sub hstart {
my ($self) = @_;
return $self->{hstart};
}
=head3 end()
End of the hit in hit sequence.
=cut
sub hstop {
my ($self) = @_;
return $self->{hstop};
}
=head3 qlength()
length of the query sequence in similarities
=cut
sub qlength {
my ($self) = @_;
return $self->{qlength};
}
=head3 hlength()
length of the hit sequence in similarities
=cut
sub hlength {
my ($self) = @_;
return $self->{hlength};
}
=head3 evalue()
E-value or P-Value if present.
=cut
sub evalue {
my ($self) = @_;
return $self->{evalue};
}
=head3 score()
Score if present.
=cut
sub score {
my ($self) = @_;
return $self->{score};
}
=head3 display()
will be different for each type
=cut
sub display {
die "Abstract Method Called\n";
}
=head3 display_table()
will be different for each type
=cut
sub display_table {
die "Abstract Table Method Called\n";
}
=head3 get_objects()
This is the B<REAL WORKHORSE> method of this Package.
=cut
sub get_objects {
my ($self,$fid,$scope) = @_;
my $objects = [];
my @matched_datasets=();
my $fig = new FIG;
# call function that fetches attribute based observations
# returns an array of arrays of hashes
if($scope){
get_cluster_observations($fid,\@matched_datasets,$scope);
}
else{
my %domain_classes;
my @attributes = $fig->get_attributes($fid);
$domain_classes{'CDD'} = 1;
#get_identical_proteins($fid,\@matched_datasets);
get_attribute_based_domain_observations($fid,\%domain_classes,\@matched_datasets,\@attributes);
get_sims_observations($fid,\@matched_datasets);
get_functional_coupling($fid,\@matched_datasets);
get_attribute_based_location_observations($fid,\@matched_datasets,\@attributes);
get_pdb_observations($fid,\@matched_datasets,\@attributes);
}
foreach my $dataset (@matched_datasets) {
my $object;
if($dataset->{'type'} eq "dom"){
$object = Observation::Domain->new($dataset);
}
if($dataset->{'class'} eq "PCH"){
$object = Observation::FC->new($dataset);
}
if ($dataset->{'class'} eq "IDENTICAL"){
$object = Observation::Identical->new($dataset);
}
if ($dataset->{'class'} eq "SIGNALP_CELLO_TMPRED"){
$object = Observation::Location->new($dataset);
}
if ($dataset->{'class'} eq "SIM"){
$object = Observation::Sims->new($dataset);
}
if ($dataset->{'class'} eq "CLUSTER"){
$object = Observation::Cluster->new($dataset);
}
if ($dataset->{'class'} eq "PDB"){
$object = Observation::PDB->new($dataset);
}
push (@$objects, $object);
}
return $objects;
}
=head3 display_housekeeping
This method returns the housekeeping data for a given peg in a table format
=cut
sub display_housekeeping {
my ($self,$fid) = @_;
my $fig = new FIG;
my $content;
my $org_name = $fig->org_of($fid);
my $org_id = $fig->orgid_of_orgname($org_name);
my $loc = $fig->feature_location($fid);
my($contig, $beg, $end) = $fig->boundaries_of($loc);
my $strand = ($beg <= $end)? '+' : '-';
my @subsystems = $fig->subsystems_for_peg($fid);
my $function = $fig->function_of($fid);
my @aliases = $fig->feature_aliases($fid);
my $taxonomy = $fig->taxonomy_of($org_id);
my @ecs = ($function =~ /\(EC\s(\d+\.[-\d+]+\.[-\d+]+\.[-\d+]+)\)/g);
$content .= qq(<b>General Protein Data</b><br><br><br><table border="0">);
$content .= qq(<tr width=15%><td >FIG ID</td><td>$fid</td></tr>\n);
$content .= qq(<tr width=15%><td >Organism Name</td><td>$org_name, $org_id</td></tr>\n);
$content .= qq(<tr><td width=15%>Taxonomy</td><td>$taxonomy</td></tr>\n);
$content .= qq(<tr width=15%><td>FIG Organism ID</td><td>$org_id</td></tr>\n);
$content .= qq(<tr width=15%><td>Gene Location</td><td>Contig $contig [$beg,$end], Strand $strand</td></tr>\n);;
$content .= qq(<tr width=15%><td>Function</td><td>$function</td></tr>\n);
if ( @ecs ) {
$content .= qq(<tr><td>EC:</td><td>);
foreach my $ec ( @ecs ) {
my $ec_name = $fig->ec_name($ec);
$content .= join(" -- ", $ec, $ec_name) . "<br>\n";
}
$content .= qq(</td></tr>\n);
}
if ( @subsystems ) {
$content .= qq(<tr><td>Subsystems</td><td>);
foreach my $subsystem ( @subsystems ) {
$content .= join(" -- ", @$subsystem) . "<br>\n";
}
}
my %groups;
if ( @aliases ) {
# get the db for each alias
foreach my $alias (@aliases){
$groups{$alias} = &get_database($alias);
}
# group ids by aliases
my %db_aliases;
foreach my $key (sort {$groups{$a} cmp $groups{$b}} keys %groups){
push (@{$db_aliases{$groups{$key}}}, $key);
}
$content .= qq(<tr><td>Aliases</td><td><table border="0">);
foreach my $key (sort keys %db_aliases){
$content .= qq(<tr><td>$key:</td><td>) . join(", ", @{$db_aliases{$key}}) . qq(</td></tr\n);
}
$content .= qq(</td></tr></table>\n);
}
$content .= qq(</table><p>\n);
return ($content);
}
=head3 get_sims_summary
This method uses as input the similarities of a peg and creates a tree view of their taxonomy
=cut
sub get_sims_summary {
my ($observation, $fid) = @_;
my $fig = new FIG;
my %families;
my @sims= $fig->nsims($fid,20000,10,"all");
foreach my $sim (@sims){
next if ($sim->[1] !~ /fig\|/);
my $genome = $fig->genome_of($sim->[1]);
my $taxonomy = $fig->taxonomy_of($fig->genome_of($sim->[1]));
my $parent_tax = "Root";
foreach my $tax (split(/\; /, $taxonomy)){
push (@{$families{children}{$parent_tax}}, $tax);
$families{parent}{$tax} = $parent_tax;
$parent_tax = $tax;
}
}
foreach my $key (keys %{$families{children}}){
$families{count}{$key} = @{$families{children}{$key}};
my %saw;
my @out = grep(!$saw{$_}++, @{$families{children}{$key}});
$families{children}{$key} = \@out;
}
return (\%families);
}
=head1 Internal Methods
These methods are not meant to be used outside of this package.
B<Please do not use them outside of this package!>
=cut
sub get_attribute_based_domain_observations{
# we read a FIG ID and a reference to an array (of arrays of hashes, see above)
my ($fid,$domain_classes,$datasets_ref,$attributes_ref) = (@_);
my $fig = new FIG;
foreach my $attr_ref (@$attributes_ref) {
# foreach my $attr_ref ($fig->get_attributes($fid)) {
my $key = @$attr_ref[1];
my @parts = split("::",$key);
my $class = $parts[0];
if($domain_classes->{$parts[0]}){
my $val = @$attr_ref[2];
if($val =~/^(\d+\.\d+|0\.0);(\d+)-(\d+)/){
my $raw_evalue = $1;
my $from = $2;
my $to = $3;
my $evalue;
if($raw_evalue =~/(\d+)\.(\d+)/){
my $part2 = 1000 - $1;
my $part1 = $2/100;
$evalue = $part1."e-".$part2;
}
else{
$evalue = "0.0";
}
my $dataset = {'class' => $class,
'acc' => $key,
'type' => "dom" ,
'evalue' => $evalue,
'start' => $from,
'stop' => $to,
'fig_id' => $fid,
'score' => $raw_evalue
};
push (@{$datasets_ref} ,$dataset);
}
}
}
}
sub get_attribute_based_location_observations{
my ($fid,$datasets_ref, $attributes_ref) = (@_);
my $fig = new FIG;
my $location_attributes = ['SignalP','CELLO','TMPRED','Phobius'];
my $dataset = {'type' => "loc",
'class' => 'SIGNALP_CELLO_TMPRED',
'fig_id' => $fid
};
foreach my $attr_ref (@$attributes_ref){
# foreach my $attr_ref ($fig->get_attributes($fid,$location_attributes)) {
my $key = @$attr_ref[1];
next if (($key !~ /SignalP/) && ($key !~ /CELLO/) && ($key !~ /TMPRED/) && ($key !~/Phobius/) );
my @parts = split("::",$key);
my $sub_class = $parts[0];
my $sub_key = $parts[1];
my $value = @$attr_ref[2];
if($sub_class eq "SignalP"){
if($sub_key eq "cleavage_site"){
my @value_parts = split(";",$value);
$dataset->{'cleavage_prob'} = $value_parts[0];
$dataset->{'cleavage_loc'} = $value_parts[1];
# print STDERR "LOC: $value_parts[1]";
}
elsif($sub_key eq "signal_peptide"){
$dataset->{'signal_peptide_score'} = $value;
}
}
elsif($sub_class eq "CELLO"){
$dataset->{'cello_location'} = $sub_key;
$dataset->{'cello_score'} = $value;
}
elsif($sub_class eq "Phobius"){
if($sub_key eq "transmembrane"){
$dataset->{'phobius_tm_locations'} = $value;
}
elsif($sub_key eq "signal"){
$dataset->{'phobius_signal_location'} = $value;
}
}
elsif($sub_class eq "TMPRED"){
my @value_parts = split(/\;/,$value);
$dataset->{'tmpred_score'} = $value_parts[0];
$dataset->{'tmpred_locations'} = $value_parts[1];
}
}
push (@{$datasets_ref} ,$dataset);
}
=head3 get_pdb_observations() (internal)
This methods sets the type and class for pdb observations
=cut
sub get_pdb_observations{
my ($fid,$datasets_ref, $attributes_ref) = (@_);
my $fig = new FIG;
foreach my $attr_ref (@$attributes_ref){
#foreach my $attr_ref ($fig->get_attributes($fid,'PDB')) {
my $key = @$attr_ref[1];
next if ( ($key !~ /PDB/));
my($key1,$key2) =split("::",$key);
my $value = @$attr_ref[2];
my ($evalue,$location) = split(";",$value);
if($evalue =~/(\d+)\.(\d+)/){
my $part2 = 1000 - $1;
my $part1 = $2/100;
$evalue = $part1."e-".$part2;
}
my($start,$stop) =split("-",$location);
my $url = @$attr_ref[3];
my $dataset = {'class' => 'PDB',
'type' => 'seq' ,
'acc' => $key2,
'evalue' => $evalue,
'start' => $start,
'stop' => $stop,
'fig_id' => $fid
};
push (@{$datasets_ref} ,$dataset);
}
}
=head3 get_cluster_observations() (internal)
This methods sets the type and class for cluster observations
=cut
sub get_cluster_observations{
my ($fid,$datasets_ref,$scope) = (@_);
my $dataset = {'class' => 'CLUSTER',
'type' => 'fc',
'context' => $scope,
'fig_id' => $fid
};
push (@{$datasets_ref} ,$dataset);
}
=head3 get_sims_observations() (internal)
This methods retrieves sims fills the internal data structures.
=cut
sub get_sims_observations{
my ($fid,$datasets_ref) = (@_);
my $fig = new FIG;
my @sims= $fig->nsims($fid,500,1e-20,"all");
my ($dataset);
my %id_list;
foreach my $sim (@sims){
my $hit = $sim->[1];
next if ($hit !~ /^fig\|/);
my @aliases = $fig->feature_aliases($hit);
foreach my $alias (@aliases){
$id_list{$alias} = 1;
}
}
my %already;
my (@new_sims, @uniprot);
foreach my $sim (@sims){
my $hit = $sim->[1];
my ($id) = ($hit) =~ /\|(.*)/;
next if (defined($already{$id}));
next if (defined($id_list{$hit}));
push (@new_sims, $sim);
$already{$id} = 1;
}
foreach my $sim (@new_sims){
my $hit = $sim->[1];
my $percent = $sim->[2];
my $evalue = $sim->[10];
my $qfrom = $sim->[6];
my $qto = $sim->[7];
my $hfrom = $sim->[8];
my $hto = $sim->[9];
my $qlength = $sim->[12];
my $hlength = $sim->[13];
my $db = get_database($hit);
my $func = $fig->function_of($hit);
my $organism = $fig->org_of($hit);
$dataset = {'class' => 'SIM',
'acc' => $hit,
'identity' => $percent,
'type' => 'seq',
'evalue' => $evalue,
'qstart' => $qfrom,
'qstop' => $qto,
'hstart' => $hfrom,
'hstop' => $hto,
'database' => $db,
'organism' => $organism,
'function' => $func,
'qlength' => $qlength,
'hlength' => $hlength,
'fig_id' => $fid
};
push (@{$datasets_ref} ,$dataset);
}
}
=head3 get_database (internal)
This method gets the database association from the sequence id
=cut
sub get_database{
my ($id) = (@_);
my ($db);
if ($id =~ /^fig\|/) { $db = "FIG" }
elsif ($id =~ /^gi\|/) { $db = "NCBI" }
elsif ($id =~ /^^[NXYZA]P_/) { $db = "RefSeq" }
elsif ($id =~ /^sp\|/) { $db = "SwissProt" }
elsif ($id =~ /^uni\|/) { $db = "UniProt" }
elsif ($id =~ /^tigr\|/) { $db = "TIGR" }
elsif ($id =~ /^pir\|/) { $db = "PIR" }
elsif (($id =~ /^kegg\|/) || ($id =~ /Spy/)) { $db = "KEGG" }
elsif ($id =~ /^tr\|/) { $db = "TrEMBL" }
elsif ($id =~ /^eric\|/) { $db = "ASAP" }
elsif ($id =~ /^img\|/) { $db = "JGI" }
return ($db);
}
=head3 get_identical_proteins() (internal)
This methods retrieves sims fills the internal data structures.
=cut
sub get_identical_proteins{
my ($fid,$datasets_ref) = (@_);
my $fig = new FIG;
my $funcs_ref;
my %id_list;
my @maps_to = grep { $_ ne $fid and $_ !~ /^xxx/ } map { $_->[0] } $fig->mapped_prot_ids($fid);
my @aliases = $fig->feature_aliases($fid);
foreach my $alias (@aliases){
$id_list{$alias} = 1;
}
foreach my $id (@maps_to) {
my ($tmp, $who);
if (($id ne $fid) && ($tmp = $fig->function_of($id)) && (! defined ($id_list{$id}))) {
$who = &get_database($id);
push(@$funcs_ref, [$id,$who,$tmp]);
}
}
my ($dataset);
my $dataset = {'class' => 'IDENTICAL',
'type' => 'seq',
'fig_id' => $fid,
'rows' => $funcs_ref
};
push (@{$datasets_ref} ,$dataset);
}
=head3 get_functional_coupling() (internal)
This methods retrieves the functional coupling of a protein given a peg ID
=cut
sub get_functional_coupling{
my ($fid,$datasets_ref) = (@_);
my $fig = new FIG;
my @funcs = ();
# initialize some variables
my($sc,$neigh);
# set default parameters for coupling and evidence
my ($bound,$sim_cutoff,$coupling_cutoff) = (5000, 1.0e-10, 4);
# get the fc data
my @fc_data = $fig->coupling_and_evidence($fid,$bound,$sim_cutoff,$coupling_cutoff,1);
# retrieve data
my @rows = map { ($sc,$neigh) = @$_;
[$sc,$neigh,scalar $fig->function_of($neigh)]
} @fc_data;
my ($dataset);
my $dataset = {'class' => 'PCH',
'type' => 'fc',
'fig_id' => $fid,
'rows' => \@rows
};
push (@{$datasets_ref} ,$dataset);
}
=head3 new (internal)
Instantiate a new object.
=cut
sub new {
my ($class,$dataset) = @_;
my $self = { class => $dataset->{'class'},
type => $dataset->{'type'},
fig_id => $dataset->{'fig_id'},
score => $dataset->{'score'},
};
bless($self,$class);
return $self;
}
=head3 identity (internal)
Returns the % identity of the similar sequence
=cut
sub identity {
my ($self) = @_;
return $self->{identity};
}
=head3 fig_id (internal)
=cut
sub fig_id {
my ($self) = @_;
return $self->{fig_id};
}
=head3 feature_id (internal)
=cut
sub feature_id {
my ($self) = @_;
return $self->{feature_id};
}
=head3 id (internal)
Returns the ID of the identical sequence
=cut
sub id {
my ($self) = @_;
return $self->{id};
}
=head3 organism (internal)
Returns the organism of the identical sequence
=cut
sub organism {
my ($self) = @_;
return $self->{organism};
}
=head3 function (internal)
Returns the function of the identical sequence
=cut
sub function {
my ($self) = @_;
return $self->{function};
}
=head3 database (internal)
Returns the database of the identical sequence
=cut
sub database {
my ($self) = @_;
return $self->{database};
}
sub score {
my ($self) = @_;
return $self->{score};
}
############################################################
############################################################
package Observation::PDB;
use base qw(Observation);
sub new {
my ($class,$dataset) = @_;
my $self = $class->SUPER::new($dataset);
$self->{acc} = $dataset->{'acc'};
$self->{evalue} = $dataset->{'evalue'};
$self->{start} = $dataset->{'start'};
$self->{stop} = $dataset->{'stop'};
bless($self,$class);
return $self;
}
=head3 display()
displays data stored in best_PDB attribute and in Ontology server for given PDB id
=cut
sub display{
my ($self,$gd) = @_;
my $fid = $self->fig_id;
my $dbmaster = DBMaster->new(-database =>'Ontology');
my $acc = $self->acc;
my ($pdb_description,$pdb_source,$pdb_ligand);
my $pdb_objs = $dbmaster->pdb->get_objects( { 'id' => $acc } );
if(!scalar(@$pdb_objs)){
$pdb_description = "not available";
$pdb_source = "not available";
$pdb_ligand = "not available";
}
else{
my $pdb_obj = $pdb_objs->[0];
$pdb_description = $pdb_obj->description;
$pdb_source = $pdb_obj->source;
$pdb_ligand = $pdb_obj->ligand;
}
my $lines = [];
my $line_data = [];
my $line_config = { 'title' => "PDB hit for $fid",
'short_title' => "best PDB",
'basepair_offset' => '1' };
my $fig = new FIG;
my $seq = $fig->get_translation($fid);
my $fid_stop = length($seq);
my $fid_element_hash = {
"title" => $fid,
"start" => '1',
"end" => $fid_stop,
"color"=> '1',
"zlayer" => '1'
};
push(@$line_data,$fid_element_hash);
my $links_list = [];
my $descriptions = [];
my $name;
$name = {"title" => 'id',
"value" => $acc};
push(@$descriptions,$name);
my $description;
$description = {"title" => 'pdb description',
"value" => $pdb_description};
push(@$descriptions,$description);
my $score;
$score = {"title" => "score",
"value" => $self->evalue};
push(@$descriptions,$score);
my $start_stop;
my $start_stop_value = $self->start."_".$self->stop;
$start_stop = {"title" => "start-stop",
"value" => $start_stop_value};
push(@$descriptions,$start_stop);
my $source;
$source = {"title" => "source",
"value" => $pdb_source};
push(@$descriptions,$source);
my $ligand;
$ligand = {"title" => "pdb ligand",
"value" => $pdb_ligand};
push(@$descriptions,$ligand);
my $link;
my $link_url ="http://www.rcsb.org/pdb/explore/explore.do?structureId=".$acc;
$link = {"link_title" => $acc,
"link" => $link_url};
push(@$links_list,$link);
my $pdb_element_hash = {
"title" => "PDB homology",
"start" => $self->start,
"end" => $self->stop,
"color"=> '6',
"zlayer" => '3',
"links_list" => $links_list,
"description" => $descriptions};
push(@$line_data,$pdb_element_hash);
$gd->add_line($line_data, $line_config);
return $gd;
}
1;
############################################################
############################################################
package Observation::Identical;
use base qw(Observation);
sub new {
my ($class,$dataset) = @_;
my $self = $class->SUPER::new($dataset);
$self->{rows} = $dataset->{'rows'};
bless($self,$class);
return $self;
}
=head3 display_table()
If available use the function specified here to display the "raw" observation.
This code will display a table for the identical protein
B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evi
dence.
=cut
sub display_table{
my ($self) = @_;
my $fig = new FIG;
my $fid = $self->fig_id;
my $rows = $self->rows;
my $cgi = new CGI;
my $all_domains = [];
my $count_identical = 0;
my $content;
foreach my $row (@$rows) {
my $id = $row->[0];
my $who = $row->[1];
my $assignment = $row->[2];
my $organism = $fig->org_of($id);
my $single_domain = [];
push(@$single_domain,$who);
push(@$single_domain,&HTML::set_prot_links($cgi,$id));
push(@$single_domain,$organism);
push(@$single_domain,$assignment);
push(@$all_domains,$single_domain);
$count_identical++;
}
if ($count_identical >0){
$content = $all_domains;
}
else{
$content = "<p>This PEG does not have any essentially identical proteins</p>";
}
return ($content);
}
1;
#########################################
#########################################
package Observation::FC;
1;
use base qw(Observation);
sub new {
my ($class,$dataset) = @_;
my $self = $class->SUPER::new($dataset);
$self->{rows} = $dataset->{'rows'};
bless($self,$class);
return $self;
}
=head3 display_table()
If available use the function specified here to display the "raw" observation.
This code will display a table for the identical protein
B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evi
dence.
=cut
sub display_table {
my ($self,$dataset) = @_;
my $fid = $self->fig_id;
my $rows = $self->rows;
my $cgi = new CGI;
my $functional_data = [];
my $count = 0;
my $content;
foreach my $row (@$rows) {
my $single_domain = [];
$count++;
# construct the score link
my $score = $row->[0];
my $toid = $row->[1];
my $link = $cgi->url(-relative => 1) . "?user=master&request=show_coupling_evidence&prot=$fid&to=$toid&SPROUT=";
my $sc_link = "<a href=$link>$score</a>";
push(@$single_domain,$sc_link);
push(@$single_domain,$row->[1]);
push(@$single_domain,$row->[2]);
push(@$functional_data,$single_domain);
}
if ($count >0){
$content = $functional_data;
}
else
{
$content = "<p>This PEG does not have any functional coupling</p>";
}
return ($content);
}
#########################################
#########################################
package Observation::Domain;
use base qw(Observation);
sub new {
my ($class,$dataset) = @_;
my $self = $class->SUPER::new($dataset);
$self->{evalue} = $dataset->{'evalue'};
$self->{acc} = $dataset->{'acc'};
$self->{start} = $dataset->{'start'};
$self->{stop} = $dataset->{'stop'};
bless($self,$class);
return $self;
}
sub display {
my ($thing,$gd) = @_;
my $lines = [];
# my $line_config = { 'title' => $thing->acc,
# 'short_title' => $thing->type,
# 'basepair_offset' => '1' };
my $color = "4";
my $line_data = [];
my $links_list = [];
my $descriptions = [];
my $db_and_id = $thing->acc;
my ($db,$id) = split("::",$db_and_id);
my $dbmaster = DBMaster->new(-database =>'Ontology');
my ($name_title,$name_value,$description_title,$description_value);
if($db eq "CDD"){
my $cdd_objs = $dbmaster->cdd->get_objects( { 'id' => $id } );
if(!scalar(@$cdd_objs)){
$name_title = "name";
$name_value = "not available";
$description_title = "description";
$description_value = "not available";
}
else{
my $cdd_obj = $cdd_objs->[0];
$name_title = "name";
$name_value = $cdd_obj->term;
$description_title = "description";
$description_value = $cdd_obj->description;
}
}
my $line_config = { 'title' => $thing->acc,
'short_title' => $name_value,
'basepair_offset' => '1' };
my $name;
$name = {"title" => $name_title,
"value" => $name_value};
push(@$descriptions,$name);
my $description;
$description = {"title" => $description_title,
"value" => $description_value};
push(@$descriptions,$description);
my $score;
$score = {"title" => "score",
"value" => $thing->evalue};
push(@$descriptions,$score);
my $link_id;
if ($thing->acc =~/\w+::(\d+)/){
$link_id = $1;
}
my $link;
my $link_url;
if ($thing->class eq "CDD"){$link_url = "http://0-www.ncbi.nlm.nih.gov.library.vu.edu.au:80/Structure/cdd/cddsrv.cgi?uid=$link_id"}
elsif($thing->class eq "PFAM"){$link_url = "http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?$link_id"}
else{$link_url = "NO_URL"}
$link = {"link_title" => $thing->acc,
"link" => $link_url};
push(@$links_list,$link);
my $element_hash = {
"title" => $thing->type,
"start" => $thing->start,
"end" => $thing->stop,
"color"=> $color,
"zlayer" => '2',
"links_list" => $links_list,
"description" => $descriptions};
push(@$line_data,$element_hash);
$gd->add_line($line_data, $line_config);
return $gd;
}
sub display_table {
my ($self,$dataset) = @_;
my $cgi = new CGI;
my $data = [];
my $count = 0;
my $content;
foreach my $thing (@$dataset) {
next if ($thing->type !~ /dom/);
my $single_domain = [];
$count++;
my $db_and_id = $thing->acc;
my ($db,$id) = split("::",$db_and_id);
my $dbmaster = DBMaster->new(-database =>'Ontology');
my ($name_title,$name_value,$description_title,$description_value);
if($db eq "CDD"){
my $cdd_objs = $dbmaster->cdd->get_objects( { 'id' => $id } );
if(!scalar(@$cdd_objs)){
$name_title = "name";
$name_value = "not available";
$description_title = "description";
$description_value = "not available";
}
else{
my $cdd_obj = $cdd_objs->[0];
$name_title = "name";
$name_value = $cdd_obj->term;
$description_title = "description";
$description_value = $cdd_obj->description;
}
}
my $location = $thing->start . " - " . $thing->stop;
push(@$single_domain,$db);
push(@$single_domain,$thing->acc);
push(@$single_domain,$name_value);
push(@$single_domain,$location);
push(@$single_domain,$thing->evalue);
push(@$single_domain,$description_value);
push(@$data,$single_domain);
}
if ($count >0){
$content = $data;
}
else
{
$content = "<p>This PEG does not have any similarities to domains</p>";
}
}
#########################################
#########################################
package Observation::Location;
use base qw(Observation);
sub new {
my ($class,$dataset) = @_;
my $self = $class->SUPER::new($dataset);
$self->{cleavage_prob} = $dataset->{'cleavage_prob'};
$self->{cleavage_loc} = $dataset->{'cleavage_loc'};
$self->{signal_peptide_score} = $dataset->{'signal_peptide_score'};
$self->{cello_location} = $dataset->{'cello_location'};
$self->{cello_score} = $dataset->{'cello_score'};
$self->{tmpred_score} = $dataset->{'tmpred_score'};
$self->{tmpred_locations} = $dataset->{'tmpred_locations'};
$self->{phobius_signal_location} = $dataset->{'phobius_signal_location'};
$self->{phobius_tm_locations} = $dataset->{'phobius_tm_locations'};
bless($self,$class);
return $self;
}
sub display {
my ($thing,$gd) = @_;
my $fid = $thing->fig_id;
my $fig= new FIG;
my $length = length($fig->get_translation($fid));
my $cleavage_prob;
if($thing->cleavage_prob){$cleavage_prob = $thing->cleavage_prob;}
my ($cleavage_loc_begin,$cleavage_loc_end) = split("-",$thing->cleavage_loc);
my $signal_peptide_score = $thing->signal_peptide_score;
my $cello_location = $thing->cello_location;
my $cello_score = $thing->cello_score;
my $tmpred_score = $thing->tmpred_score;
my @tmpred_locations = split(",",$thing->tmpred_locations);
my $phobius_signal_location = $thing->phobius_signal_location;
my @phobius_tm_locations = split(",",$thing->phobius_tm_locations);
my $lines = [];
#color is
my $color = "6";
if($cello_location){
my $cello_descriptions = [];
my $line_data =[];
my $line_config = { 'title' => 'Localization Evidence',
'short_title' => 'CELLO',
'basepair_offset' => '1' };
my $description_cello_location = {"title" => 'Best Cello Location',
"value" => $cello_location};
push(@$cello_descriptions,$description_cello_location);
my $description_cello_score = {"title" => 'Cello Score',
"value" => $cello_score};
push(@$cello_descriptions,$description_cello_score);
my $element_hash = {
"title" => "CELLO",
"start" => "1",
"end" => $length + 1,
"color"=> $color,
"type" => 'box',
"zlayer" => '1',
"description" => $cello_descriptions};
push(@$line_data,$element_hash);
$gd->add_line($line_data, $line_config);
}
$color = "2";
if($tmpred_score){
my $line_data =[];
my $line_config = { 'title' => 'Localization Evidence',
'short_title' => 'Transmembrane',
'basepair_offset' => '1' };
foreach my $tmpred (@tmpred_locations){
my $descriptions = [];
my ($begin,$end) =split("-",$tmpred);
my $description_tmpred_score = {"title" => 'TMPRED score',
"value" => $tmpred_score};
push(@$descriptions,$description_tmpred_score);
my $element_hash = {
"title" => "transmembrane location",
"start" => $begin + 1,
"end" => $end + 1,
"color"=> $color,
"zlayer" => '5',
"type" => 'smallbox',
"description" => $descriptions};
push(@$line_data,$element_hash);
}
$gd->add_line($line_data, $line_config);
}
if((scalar(@phobius_tm_locations) > 0) || $phobius_signal_location){
my $line_data =[];
my $line_config = { 'title' => 'Localization Evidence',
'short_title' => 'Phobius',
'basepair_offset' => '1' };
foreach my $tm_loc (@phobius_tm_locations){
my $descriptions = [];
my $description_phobius_tm_locations = {"title" => 'Phobius TM Location',
"value" => $tm_loc};
push(@$descriptions,$description_phobius_tm_locations);
my ($begin,$end) =split("-",$tm_loc);
my $element_hash = {
"title" => "phobius transmembrane location",
"start" => $begin + 1,
"end" => $end + 1,
"color"=> '6',
"zlayer" => '4',
"type" => 'bigbox',
"description" => $descriptions};
push(@$line_data,$element_hash);
}
if($phobius_signal_location){
my $descriptions = [];
my $description_phobius_signal_location = {"title" => 'Phobius Signal Location',
"value" => $phobius_signal_location};
push(@$descriptions,$description_phobius_signal_location);
my ($begin,$end) =split("-",$phobius_signal_location);
my $element_hash = {
"title" => "phobius signal locations",
"start" => $begin + 1,
"end" => $end + 1,
"color"=> '1',
"zlayer" => '5',
"type" => 'box',
"description" => $descriptions};
push(@$line_data,$element_hash);
}
$gd->add_line($line_data, $line_config);
}
$color = "1";
if($signal_peptide_score){
my $line_data = [];
my $descriptions = [];
my $line_config = { 'title' => 'Localization Evidence',
'short_title' => 'SignalP',
'basepair_offset' => '1' };
my $description_signal_peptide_score = {"title" => 'signal peptide score',
"value" => $signal_peptide_score};
push(@$descriptions,$description_signal_peptide_score);
my $description_cleavage_prob = {"title" => 'cleavage site probability',
"value" => $cleavage_prob};
push(@$descriptions,$description_cleavage_prob);
my $element_hash = {
"title" => "SignalP",
"start" => $cleavage_loc_begin - 2,
"end" => $cleavage_loc_end + 1,
"type" => 'bigbox',
"color"=> $color,
"zlayer" => '10',
"description" => $descriptions};
push(@$line_data,$element_hash);
$gd->add_line($line_data, $line_config);
}
return ($gd);
}
sub cleavage_loc {
my ($self) = @_;
return $self->{cleavage_loc};
}
sub cleavage_prob {
my ($self) = @_;
return $self->{cleavage_prob};
}
sub signal_peptide_score {
my ($self) = @_;
return $self->{signal_peptide_score};
}
sub tmpred_score {
my ($self) = @_;
return $self->{tmpred_score};
}
sub tmpred_locations {
my ($self) = @_;
return $self->{tmpred_locations};
}
sub cello_location {
my ($self) = @_;
return $self->{cello_location};
}
sub cello_score {
my ($self) = @_;
return $self->{cello_score};
}
sub phobius_signal_location {
my ($self) = @_;
return $self->{phobius_signal_location};
}
sub phobius_tm_locations {
my ($self) = @_;
return $self->{phobius_tm_locations};
}
#########################################
#########################################
package Observation::Sims;
use base qw(Observation);
sub new {
my ($class,$dataset) = @_;
my $self = $class->SUPER::new($dataset);
$self->{identity} = $dataset->{'identity'};
$self->{acc} = $dataset->{'acc'};
$self->{evalue} = $dataset->{'evalue'};
$self->{qstart} = $dataset->{'qstart'};
$self->{qstop} = $dataset->{'qstop'};
$self->{hstart} = $dataset->{'hstart'};
$self->{hstop} = $dataset->{'hstop'};
$self->{database} = $dataset->{'database'};
$self->{organism} = $dataset->{'organism'};
$self->{function} = $dataset->{'function'};
$self->{qlength} = $dataset->{'qlength'};
$self->{hlength} = $dataset->{'hlength'};
bless($self,$class);
return $self;
}
=head3 display()
If available use the function specified here to display a graphical observation.
This code will display a graphical view of the similarities using the genome drawer object
=cut
sub display {
my ($self,$gd) = @_;
my $fig = new FIG;
my $peg = $self->acc;
my $organism = $self->organism;
my $genome = $fig->genome_of($peg);
my ($org_tax) = ($genome) =~ /(.*)\./;
my $function = $self->function;
my $abbrev_name = $fig->abbrev($organism);
my $align_start = $self->qstart;
my $align_stop = $self->qstop;
my $hit_start = $self->hstart;
my $hit_stop = $self->hstop;
my $tax_link = "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=" . $org_tax;
my $line_config = { 'title' => "$organism [$org_tax]",
'short_title' => "$abbrev_name",
'title_link' => '$tax_link',
'basepair_offset' => '0'
};
my $line_data = [];
my $element_hash;
my $links_list = [];
my $descriptions = [];
# get subsystem information
my $url_link = "http://seed-viewer.theseed.org/index.cgi?action=ShowAnnotation&prot=".$peg;
my $link;
$link = {"link_title" => $peg,
"link" => $url_link};
push(@$links_list,$link);
my @subsystems = $fig->peg_to_subsystems($peg);
foreach my $subsystem (@subsystems){
my $link;
$link = {"link" => "http://seed-viewer.theseed.org/index.cgi?action=ShowSubsystem&subsystem_name=$subsystem",
"link_title" => $subsystem};
push(@$links_list,$link);
}
my $description_function;
$description_function = {"title" => "function",
"value" => $function};
push(@$descriptions,$description_function);
my ($description_ss, $ss_string);
$ss_string = join (",", @subsystems);
$description_ss = {"title" => "subsystems",
"value" => $ss_string};
push(@$descriptions,$description_ss);
my $description_loc;
$description_loc = {"title" => "location start",
"value" => $hit_start};
push(@$descriptions, $description_loc);
$description_loc = {"title" => "location stop",
"value" => $hit_stop};
push(@$descriptions, $description_loc);
my $evalue = $self->evalue;
while ($evalue =~ /-0/)
{
my ($chunk1, $chunk2) = split(/-/, $evalue);
$chunk2 = substr($chunk2,1);
$evalue = $chunk1 . "-" . $chunk2;
}
my $color = &color($evalue);
my $description_eval = {"title" => "E-Value",
"value" => $evalue};
push(@$descriptions, $description_eval);
my $identity = $self->identity;
my $description_identity = {"title" => "Identity",
"value" => $identity};
push(@$descriptions, $description_identity);
$element_hash = {
"title" => $peg,
"start" => $align_start,
"end" => $align_stop,
"type"=> 'box',
"color"=> $color,
"zlayer" => "2",
"links_list" => $links_list,
"description" => $descriptions
};
push(@$line_data,$element_hash);
$gd->add_line($line_data, $line_config);
return ($gd);
}
=head3 display_table()
If available use the function specified here to display the "raw" observation.
This code will display a table for the similarities protein
B<Please note> that URL linked to in display_method() is an external component and needs to added to the code for every class of evidence.
=cut
sub display_table {
my ($self,$dataset, $columns, $query_fid) = @_;
my $data = [];
my $count = 0;
my $content;
my $fig = new FIG;
my $cgi = new CGI;
my @ids;
foreach my $thing (@$dataset) {
next if ($thing->class ne "SIM");
push (@ids, $thing->acc);
}
my (%box_column, %subsystems_column, %evidence_column, %e_identical);
foreach my $col (@$columns){
# get the column for the subsystems
if ($col eq "subsystem"){
%subsystems_column = &get_subsystems_column(\@ids);
}
# get the column for the evidence codes
elsif ($col eq "evidence"){
%evidence_column = &get_evidence_column(\@ids);
}
}
my %e_identical = &get_essentially_identical($query_fid);
foreach my $thing (@$dataset) {
next if ($thing->class ne "SIM");
my $single_domain = [];
$count++;
my $id = $thing->acc;
my $iden = $thing->identity;
my $ln1 = $thing->qlength;
my $ln2 = $thing->hlength;
my $b1 = $thing->qstart;
my $e1 = $thing->qstop;
my $b2 = $thing->hstart;
my $e2 = $thing->hstop;
my $d1 = abs($e1 - $b1) + 1;
my $d2 = abs($e2 - $b2) + 1;
my $reg1 = "$b1-$e1 (<b>$d1/$ln1</b>)";
my $reg2 = "$b2-$e2 (<b>$d2/$ln2</b>)";
# checkbox column
my $field_name = "tables_" . $id;
my $pair_name = "visual_" . $id;
my $box_col = qq(<input type=checkbox name=seq value="$id" id="$field_name" onClick="VisualCheckPair('$field_name', '$pair_name');">);
# get the linked fig id
my $fig_col;
if (defined ($e_identical{$id})){
$fig_col = &HTML::set_prot_links($cgi,$id) . "*";
}
else{
$fig_col = &HTML::set_prot_links($cgi,$id);
}
push(@$single_domain,$box_col); # permanent column
push(@$single_domain,$fig_col); # permanent column
push(@$single_domain,$thing->evalue); # permanent column
push(@$single_domain,"$iden\%"); # permanent column
push(@$single_domain,$reg1); # permanent column
push(@$single_domain,$reg2); # permanent column
push(@$single_domain,$thing->organism); # permanent column
push(@$single_domain,$thing->function); # permanent column
foreach my $col (@$columns){
(push(@$single_domain,$subsystems_column{$id}) && (next)) if ($col eq "subsystem");
(push(@$single_domain,$evidence_column{$id}) && (next)) if ($col eq "evidence");
(push(@$single_domain,&get_prefer($thing->acc, 'NCBI')) && (next)) if ($col eq "ncbi_id");
(push(@$single_domain,&get_prefer($thing->acc, 'RefSeq')) && (next)) if ($col eq "refseq_id");
(push(@$single_domain,&get_prefer($thing->acc, 'SwissProt')) && (next)) if ($col eq "swissprot_id");
(push(@$single_domain,&get_prefer($thing->acc, 'UniProt')) && (next)) if ($col eq "uniprot_id");
(push(@$single_domain,&get_prefer($thing->acc, 'TIGR')) && (next)) if ($col eq "tigr_id");
(push(@$single_domain,&get_prefer($thing->acc, 'PIR')) && (next)) if ($col eq "pir_id");
(push(@$single_domain,&get_prefer($thing->acc, 'KEGG')) && (next)) if ($col eq "kegg_id");
(push(@$single_domain,&get_prefer($thing->acc, 'TrEMBL')) && (next)) if ($col eq "trembl_id");
(push(@$single_domain,&get_prefer($thing->acc, 'ASAP')) && (next)) if ($col eq "asap_id");
(push(@$single_domain,&get_prefer($thing->acc, 'JGI')) && (next)) if ($col eq "jgi_id");
}
push(@$data,$single_domain);
}
if ($count >0 ){
$content = $data;
}
else{
$content = "<p>This PEG does not have any similarities</p>";
}
return ($content);
}
sub get_box_column{
my ($ids) = @_;
my %column;
foreach my $id (@$ids){
my $field_name = "tables_" . $id;
my $pair_name = "visual_" . $id;
$column{$id} = qq(<input type=checkbox name=seq value="$id" id="$field_name" onClick="VisualCheckPair('$field_name', '$pair_name');">);
}
return (%column);
}
sub get_subsystems_column{
my ($ids) = @_;
my $fig = new FIG;
my $cgi = new CGI;
my %in_subs = $fig->subsystems_for_pegs($ids);
my %column;
foreach my $id (@$ids){
my @in_sub = @{$in_subs{$id}} if (defined $in_subs{$id});
my @subsystems;
if (@in_sub > 0) {
my $count = 1;
foreach my $array(@in_sub){
push (@subsystems, $count . ". " . $$array[0]);
$count++;
}
my $in_sub_line = join ("<br>", @subsystems);
$column{$id} = $in_sub_line;
} else {
$column{$id} = " ";
}
}
return (%column);
}
sub get_essentially_identical{
my ($fid) = @_;
my $fig = new FIG;
my %id_list;
my @maps_to = grep { $_ ne $fid and $_ !~ /^xxx/ } map { $_->[0] } $fig->mapped_prot_ids($fid);
foreach my $id (@maps_to) {
if (($id ne $fid) && ($fig->function_of($id))) {
$id_list{$id} = 1;
}
}
return(%id_list);
}
sub get_evidence_column{
my ($ids) = @_;
my $fig = new FIG;
my $cgi = new CGI;
my (%column, %code_attributes);
my @codes = grep { $_->[1] =~ /^evidence_code/i } $fig->get_attributes($ids);
foreach my $key (@codes){
push (@{$code_attributes{$$key[0]}}, $key);
}
foreach my $id (@$ids){
# add evidence code with tool tip
my $ev_codes=" ";
my @ev_codes = "";
if ($id =~ /^fig\|\d+\.\d+\.peg\.\d+$/) {
my @codes;
@codes = @{$code_attributes{$id}} if (defined @{$code_attributes{$id}});
@ev_codes = ();
foreach my $code (@codes) {
my $pretty_code = $code->[2];
if ($pretty_code =~ /;/) {
my ($cd, $ss) = split(";", $code->[2]);
$ss =~ s/_/ /g;
$pretty_code = $cd;# . " in " . $ss;
}
push(@ev_codes, $pretty_code);
}
}
if (scalar(@ev_codes) && $ev_codes[0]) {
my $ev_code_help=join("<br />", map {&HTML::evidence_codes_explain($_)} @ev_codes);
$ev_codes = $cgi->a(
{
id=>"evidence_codes", onMouseover=>"javascript:if(!this.tooltip) this.tooltip=new Popup_Tooltip(this, 'Evidence Codes', '$ev_code_help', ''); this.tooltip.addHandler(); return false;"}, join("<br />", @ev_codes));
}
$column{$id}=$ev_codes;
}
return (%column);
}
sub html_enc { $_ = $_[0]; s/\&/&/g; s/\>/>/g; s/\</</g; $_ }
sub get_prefer {
my ($fid, $db) = @_;
my $fig = new FIG;
my $cgi = new CGI;
my @aliases = $fig->feature_aliases($fid);
foreach my $alias (@aliases){
my $id_db = &Observation::get_database($alias);
if ($id_db eq $db){
my $acc_col .= &HTML::set_prot_links($cgi,$alias);
return ($acc_col);
}
}
return (" ");
}
sub color {
my ($evalue) = @_;
my $color;
if ($evalue <= 1e-170){
$color = 51;
}
elsif (($evalue <= 1e-120) && ($evalue > 1e-170)){
$color = 52;
}
elsif (($evalue <= 1e-90) && ($evalue > 1e-120)){
$color = 53;
}
elsif (($evalue <= 1e-70) && ($evalue > 1e-90)){
$color = 54;
}
elsif (($evalue <= 1e-40) && ($evalue > 1e-70)){
$color = 55;
}
elsif (($evalue <= 1e-20) && ($evalue > 1e-40)){
$color = 56;
}
elsif (($evalue <= 1e-5) && ($evalue > 1e-20)){
$color = 57;
}
elsif (($evalue <= 1) && ($evalue > 1e-5)){
$color = 58;
}
elsif (($evalue <= 10) && ($evalue > 1)){
$color = 59;
}
else{
$color = 60;
}
return ($color);
}
############################
package Observation::Cluster;
use base qw(Observation);
sub new {
my ($class,$dataset) = @_;
my $self = $class->SUPER::new($dataset);
$self->{context} = $dataset->{'context'};
bless($self,$class);
return $self;
}
sub display {
my ($self,$gd) = @_;
my $fid = $self->fig_id;
my $compare_or_coupling = $self->context;
my $gd_window_size = $gd->window_size;
my $fig = new FIG;
my $all_regions = [];
#get the organism genome
my $target_genome = $fig->genome_of($fid);
# get location of the gene
my $data = $fig->feature_location($fid);
my ($contig, $beg, $end);
my %reverse_flag;
if ($data =~ /(.*)_(\d+)_(\d+)$/){
$contig = $1;
$beg = $2;
$end = $3;
}
my $offset;
my ($region_start, $region_end);
if ($beg < $end)
{
$region_start = $beg - 4000;
$region_end = $end+4000;
$offset = ($2+(($3-$2)/2))-($gd_window_size/2);
}
else
{
$region_start = $end-4000;
$region_end = $beg+4000;
$offset = ($3+(($2-$3)/2))-($gd_window_size/2);
$reverse_flag{$target_genome} = $fid;
}
# call genes in region
my ($target_gene_features, $reg_beg, $reg_end) = $fig->genes_in_region($target_genome, $contig, $region_start, $region_end);
push(@$all_regions,$target_gene_features);
my (@start_array_region);
push (@start_array_region, $offset);
my %all_genes;
my %all_genomes;
foreach my $feature (@$target_gene_features){ $all_genes{$feature} = $fid;}
if ($compare_or_coupling eq "diverse")
{
my @coup = grep { $_->[1]} $fig->coupling_and_evidence($fid,5000,1e-10,4,1);
my $coup_count = 0;
foreach my $pair (@{$coup[0]->[2]}) {
# last if ($coup_count > 10);
my ($peg1,$peg2) = @$pair;
my ($pair_contig,$pair_beg,$pair_end,$pair_region_start,$pair_region_stop,$pair_genome);
$pair_genome = $fig->genome_of($peg1);
my $location = $fig->feature_location($peg1);
if($location =~/(.*)_(\d+)_(\d+)$/){
$pair_contig = $1;
$pair_beg = $2;
$pair_end = $3;
if ($pair_beg < $pair_end)
{
$pair_region_start = $pair_beg - 4000;
$pair_region_stop = $pair_end+4000;
$offset = ($2+(($3-$2)/2))-($gd_window_size/2);
}
else
{
$pair_region_start = $pair_end-4000;
$pair_region_stop = $pair_beg+4000;
$offset = ($3+(($2-$3)/2))-($gd_window_size/2);
$reverse_flag{$pair_genome} = $peg1;
}
push (@start_array_region, $offset);
$all_genomes{$pair_genome} = 1;
my ($pair_features) = $fig->genes_in_region($pair_genome, $pair_contig, $pair_region_start, $pair_region_stop);
push(@$all_regions,$pair_features);
foreach my $pair_feature (@$pair_features){ $all_genes{$pair_feature} = $peg1;}
}
$coup_count++;
}
}
elsif ($compare_or_coupling eq "close")
{
# make a hash of genomes that are phylogenetically close
#my $close_threshold = ".26";
#my @genomes = $fig->genomes('complete');
#my %close_genomes = ();
#foreach my $compared_genome (@genomes)
#{
# my $dist = $fig->crude_estimate_of_distance($target_genome,$compared_genome);
# #$close_genomes{$compared_genome} = $dist;
# if ($dist <= $close_threshold)
# {
# $all_genomes{$compared_genome} = 1;
# }
#}
$all_genomes{"216592.1"} = 1;
$all_genomes{"79967.1"} = 1;
$all_genomes{"199310.1"} = 1;
$all_genomes{"216593.1"} = 1;
$all_genomes{"155864.1"} = 1;
$all_genomes{"83334.1"} = 1;
$all_genomes{"316407.3"} = 1;
foreach my $comp_genome (keys %all_genomes){
my $return = $fig->bbh_list($comp_genome,[$fid]);
my $feature_list = $return->{$fid};
foreach my $peg1 (@$feature_list){
my $location = $fig->feature_location($peg1);
my ($pair_contig,$pair_beg,$pair_end,$pair_region_start,$pair_region_stop,$pair_genome);
$pair_genome = $fig->genome_of($peg1);
if($location =~/(.*)_(\d+)_(\d+)$/){
$pair_contig = $1;
$pair_beg = $2;
$pair_end = $3;
if ($pair_beg < $pair_end)
{
$pair_region_start = $pair_beg - 4000;
$pair_region_stop = $pair_end + 4000;
$offset = ($2+(($3-$2)/2))-($gd_window_size/2);
}
else
{
$pair_region_start = $pair_end-4000;
$pair_region_stop = $pair_beg+4000;
$offset = ($3+(($2-$3)/2))-($gd_window_size/2);
$reverse_flag{$pair_genome} = $peg1;
}
push (@start_array_region, $offset);
$all_genomes{$pair_genome} = 1;
my ($pair_features) = $fig->genes_in_region($pair_genome, $pair_contig, $pair_region_start, $pair_region_stop);
push(@$all_regions,$pair_features);
foreach my $pair_feature (@$pair_features){ $all_genes{$pair_feature} = $peg1;}
}
}
}
}
# get the PCH to each of the genes
my $pch_sets = [];
my %pch_already;
foreach my $gene_peg (keys %all_genes)
{
if ($pch_already{$gene_peg}){(next);};
my $gene_set = [$gene_peg];
foreach my $pch_peg ($fig->in_pch_pin_with($gene_peg)) {
$pch_peg =~ s/,.*$//;
my $pch_genome = $fig->genome_of($pch_peg);
if ( ($gene_peg ne $pch_peg) && ($all_genomes{$pch_genome})) {
push(@$gene_set,$pch_peg);
$pch_already{$pch_peg}=1;
}
$pch_already{$gene_peg}=1;
}
push(@$pch_sets,$gene_set);
}
#create a rank of the pch's
my %pch_set_rank;
my $order = 0;
foreach my $set (@$pch_sets){
my $count = scalar(@$set);
$pch_set_rank{$order} = $count;
$order++;
}
my %peg_rank;
my $counter = 1;
foreach my $pch_order (sort {$pch_set_rank{$b} <=> $pch_set_rank{$a}} keys %pch_set_rank){
my $good_set = @$pch_sets[$pch_order];
my $flag_set = 0;
if (scalar (@$good_set) > 1)
{
foreach my $peg (@$good_set){
if ((!$peg_rank{$peg})){
$peg_rank{$peg} = $counter;
$flag_set = 1;
}
}
$counter++ if ($flag_set == 1);
}
else
{
foreach my $peg (@$good_set){
$peg_rank{$peg} = "20";
}
}
}
# my $bbh_sets = [];
# my %already;
# foreach my $gene_key (keys(%all_genes)){
# if($already{$gene_key}){(next);}
# my $gene_set = [$gene_key];
#
# my $gene_key_genome = $fig->genome_of($gene_key);
#
# foreach my $genome_key (keys(%all_genomes)){
# #(next) if ($gene_key_genome eq $genome_key);
# my $return = $fig->bbh_list($genome_key,[$gene_key]);
#
# my $feature_list = $return->{$gene_key};
# foreach my $fl (@$feature_list){
# push(@$gene_set,$fl);
# }
# }
# $already{$gene_key} = 1;
# push(@$bbh_sets,$gene_set);
# }
#
# my %bbh_set_rank;
# my $order = 0;
# foreach my $set (@$bbh_sets){
# my $count = scalar(@$set);
# $bbh_set_rank{$order} = $count;
# $order++;
# }
#
# my %peg_rank;
# my $counter = 1;
# foreach my $bbh_order (sort {$bbh_set_rank{$b} <=> $bbh_set_rank{$a}} keys %bbh_set_rank){
# my $good_set = @$bbh_sets[$bbh_order];
# my $flag_set = 0;
# if (scalar (@$good_set) > 1)
# {
# foreach my $peg (@$good_set){
# if ((!$peg_rank{$peg})){
# $peg_rank{$peg} = $counter;
# $flag_set = 1;
# }
# }
# $counter++ if ($flag_set == 1);
# }
# else
# {
# foreach my $peg (@$good_set){
# $peg_rank{$peg} = "20";
# }
# }
# }
foreach my $region (@$all_regions){
my $sample_peg = @$region[0];
my $region_genome = $fig->genome_of($sample_peg);
my $region_gs = $fig->genus_species($region_genome);
my $abbrev_name = $fig->abbrev($region_gs);
my $line_config = { 'title' => $region_gs,
'short_title' => $abbrev_name,
'basepair_offset' => '0'
};
my $offsetting = shift @start_array_region;
my $second_line_config = { 'title' => "$region_gs",
'short_title' => "",
'basepair_offset' => '0'
};
my $line_data = [];
my $second_line_data = [];
# initialize variables to check for overlap in genes
my ($prev_start, $prev_stop, $prev_fig, $second_line_flag);
my $major_line_flag = 0;
my $prev_second_flag = 0;
foreach my $fid1 (@$region){
$second_line_flag = 0;
my $element_hash;
my $links_list = [];
my $descriptions = [];
my $color = $peg_rank{$fid1};
# get subsystem information
my $function = $fig->function_of($fid1);
my $url_link = "http://seed-viewer.theseed.org/index.cgi?action=ShowAnnotation&prot=".$fid1;
my $link;
$link = {"link_title" => $fid1,
"link" => $url_link};
push(@$links_list,$link);
my @subsystems = $fig->peg_to_subsystems($fid1);
foreach my $subsystem (@subsystems){
my $link;
$link = {"link" => "http://seed-viewer.theseed.org/index.cgi?action=ShowSubsystem&subsystem_name=$subsystem",
"link_title" => $subsystem};
push(@$links_list,$link);
}
my $description_function;
$description_function = {"title" => "function",
"value" => $function};
push(@$descriptions,$description_function);
my $description_ss;
my $ss_string = join (",", @subsystems);
$description_ss = {"title" => "subsystems",
"value" => $ss_string};
push(@$descriptions,$description_ss);
my $fid_location = $fig->feature_location($fid1);
if($fid_location =~/(.*)_(\d+)_(\d+)$/){
my($start,$stop);
$start = $2 - $offsetting;
$stop = $3 - $offsetting;
if ( (($prev_start) && ($prev_stop) ) &&
( ($start < $prev_start) || ($start < $prev_stop) ||
($stop < $prev_start) || ($stop < $prev_stop) )){
if (($second_line_flag == 0) && ($prev_second_flag == 0)) {
$second_line_flag = 1;
$major_line_flag = 1;
}
}
$prev_start = $start;
$prev_stop = $stop;
$prev_fig = $fid1;
if ((defined($reverse_flag{$region_genome})) && ($reverse_flag{$region_genome} eq $all_genes{$fid1})){
$start = $gd_window_size - $start;
$stop = $gd_window_size - $stop;
}
$element_hash = {
"title" => $fid1,
"start" => $start,
"end" => $stop,
"type"=> 'arrow',
"color"=> $color,
"zlayer" => "2",
"links_list" => $links_list,
"description" => $descriptions
};
# if there is an overlap, put into second line
if ($second_line_flag == 1){ push(@$second_line_data,$element_hash); $prev_second_flag = 1;}
else{ push(@$line_data,$element_hash); $prev_second_flag = 0;}
}
}
$gd->add_line($line_data, $line_config);
$gd->add_line($second_line_data, $second_line_config) if ($major_line_flag == 1);
}
return $gd;
}
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