#!/usr/bin/perl
package ExpressionConnection;
#######################################################################
##### Author : Shuai Weng
##### Date : Nov. 2002
##### Description : This package contains all necessary methods for
##### searching gene expression data from multiple
##### microarray studies.
#####
#######################################################################
use strict;
use DBI;
use CGI qw/:all :html3/;
use GD;
use lib "/usr/local/dicty/www_dictybase/db/lib/dictyBase/Objects";
use ConfigURLdictyBase;
use ConfigPathdictyBase;
use SeqParamTranslator;
use Dataset;
use Feature;
use CreateGD;
use lib "/usr/local/dicty/www_dictybase/db/lib/common";
use Login qw (ConnectToDatabase);
use TextUtil qw (DeleteUnwantedChar);
use lib "/usr/local/dicty/www_dictybase/db/lib/dictyBase";
use dictyBaseCentralMod qw(:formatPage);
use dictyBaseObject;
use lib "/usr/local/dicty/www_dictybase/db/lib/dictyBase/Objects/MAP";
use MapUtil;
#######################################################################
#################### global variables #################################
#######################################################################
my $dbh;
my $dblink;
my $configUrl;
my $configPath;
my $cubeImage;
my $loci;
my @orf;
my @dataset;
my $sortBy;
my $exprtype;
my $fold;
my %datasetTitle;
my %featNo4featNm;
my %featNo4featNmInAll;
my %featNm4geneInAll;
my %maxExprVal4featNm;
my %minExprVal4featNm;
my %gene4featNm;
my %gene4featNmInAll;
my %genes4dataset;
my %expts4dataset;
my %geneNum4dataset;
my $locusUrl;
my $maxDisplayNum = 20;
my $totalGene;
#######################################################################
sub new { ############ constructor ###############################
#######################################################################
my ($self, %args) = @_;
$self = {};
bless $self;
$self->{'_database'} = $args{'database'};
$self->{'_help'} = $args{'help'};
$self->{'_title'} = $args{'title'} || "Expression Connection";
$dbh = &ConnectToDatabase($self->{'_database'});
return $self;
}
######################################################################
sub help { $_[0]->{_help} }
sub database { $_[0]->{_database} }
sub title { $_[0]->{_title} }
######################################################################
sub start{
######################################################################
my ($self) = @_;
$self->setVariables;
if (!param || param('newSearchSubmit') || param('ORFs')) {
$self->printEntryForm;
exit;
}
if (param('query') && param('noSearch')) {
param('loci', param('query'));
$self->printEntryForm;
exit;
}
$self->setHelp;
$self->choosePageToPrint;
exit;
}
#######################################################################
sub printEntryForm {
#######################################################################
my ($self) = shift;
&printStartPage($self->database, $self->title, $self->help);
$self->printDescription;
$self->printOption1;
$self->printOption2;
$self->printOption3;
# $self->additionalSearch;
&printEndPage;
}
########################################################################
sub setHelp {
########################################################################
my ($self) = @_;
if (param('type') =~ /^histogram/i) {
$self->{'_help'} .= "#histograph";
}
elsif (param('type') =~ /^graph/i) {
$self->{'_help'} .= "#graph";
}
elsif (param('type') =~ /^Pearson/i) {
$self->{'_help'} .= "#pearson";
}
}
########################################################################
sub choosePageToPrint {
########################################################################
my ($self) = @_;
&printStartPage($self->database, $self->title, $self->help);
if (param('submit1') || param('option') =~ /option1/i) {
$self->showResultForOption1;
}
elsif (param('orf') && param('dataset') && !param('type')) {
# $self->showResultForOption1;
$self->showSimilarResult;
}
elsif (param('submit2') || param('option') =~ /option2/i) {
$self->showResultForOption2;
}
elsif (param('submit3') || param('option') =~ /option3/i) {
$self->showResultForOption3;
}
elsif (param('downloadSubmit')) {
$self->showDownloadList;
}
elsif (param('type') =~ /^statistic/i) {
$self->showStatisticForDataset;
}
elsif (param('type') =~ /^histogram/i) {
$self->showHistogramForGene;
}
elsif (param('type') =~ /^enlarge/i) {
$self->showEnlargeResult;
}
elsif (param('type') =~ /^similar/i) {
$self->showSimilarResult;
}
elsif (param('type') =~ /^graph/i) {
$self->showGraph;
}
elsif (param('type') =~ /^Pearson/i) {
$self->showPearsonCorrelation;
}
elsif (param('type') =~ /^regulatedBy/i) {
$self->showRegulatorList;
}
elsif (param('type') =~ /^regulator/i) {
$self->showRegulationModuleList;
}
elsif (param('more') && param('id')) {
$self->showGeneList;
}
elsif (param('sortSubmit') || param('wholeSubmit')) {
$self->sortAndShowResult;
}
elsif (param('orf') && param('fold')) {
$self->showDatasetExpt;
}
else {
print p, "Unknown display parameter.", p;
}
if ($self->{'_error'}) {
print p, $self->{'_error'}, p;
}
&printEndPage;
}
########################################################################
sub showResultForOption1 {
########################################################################
my ($self) = @_;
$self->printSubtitle("Your Search Parameters");
$self->printSearchParamForOption1;
$self->lineSeparator;
$self->printSubtitle("Results");
$self->printScaleEtc1;
# my $rows;
foreach my $dataset (@dataset) {
### in order to associate this link to each table,
### we have to print one table at a time
print "";
print table({-border=>'0',
-cellspacing=>'1',
-cellpadding=>'2'},
$self->getResultForDataset($dataset));
if ($self->{'_noData'}{$dataset}) {
$self->{'_noData'}{$dataset} =~ s/^://;
$self->{'_noData'}{$dataset} =~ s/\:/, /g;
$self->{'_noData'}{$dataset}
=~ s/^(.+, [^\,]+,) ([^\,]+)$/$1 and $2/;
$self->{'_noData'}{$dataset}
=~ s/^([^\,]+), ([^\,]+)$/$1 and $2/;
print p, "No expression data found for ".$self->{'_noData'}{$dataset}." in this dataset.", p;
}
# $rows .= $self->getResultForDataset($dataset);
}
# print table({-border=>'0',
# -cellspacing=>'1',
# -cellpadding=>'2'},
# $rows);
$self->lineSeparator;
}
########################################################################
sub showResultForOption2 {
########################################################################
my ($self) = @_;
$self->printSubtitle("Your Search Parameters");
$self->printSearchParamForOption2;
$self->lineSeparator;
$self->printSubtitle("Results");
if ($exprtype =~ /No Data/i) {
foreach my $orf (@orf) {
$self->printNoDataResultForOrf($orf);
}
}
else {
$self->printScaleEtc2;
foreach my $orf (@orf) {
$self->printResultForOrf($orf);
}
}
$self->lineSeparator;
}
########################################################################
sub showResultForOption3 {
########################################################################
my ($self) = @_;
$self->printSubtitle("Your Search Parameters");
# $self->printSearchParamForOption3;
# $self->lineSeparator;
# $self->printSubtitle("Results");
if ($exprtype =~ /No Data/i) {
$self->printSearchParamForOption3;
$self->lineSeparator;
$self->printSubtitle("Results");
foreach my $dataset (@dataset) {
$self->printNoDataResultForDataset($dataset);
}
}
else {
# $self->printScaleEtc3;
my %tables;
my $count;
foreach my $dataset (@dataset) {
$count++;
my $id = $$.$count.$count;
$tables{$dataset} = table({-border=>'0',
-cellspacing=>'1',
-cellpadding=>'2'},
$self->getResultForDataset($dataset, $id));
# print "Total $totalGene genes found in $dataset",p;
}
$self->printSearchParamForOption3;
$self->lineSeparator;
$self->printSubtitle("Results");
$self->printScaleEtc3;
### in order to associate each dataset anchor to
### each table, we have to go over the dataset
### array one more time ...
foreach my $dataset (@dataset) {
print "";
print $tables{$dataset};
}
}
$self->lineSeparator;
}
########################################################################
sub showDatasetExpt {
########################################################################
my ($self) = @_;
my $orf = param('orf');
my $fold = param('fold');
&DeleteUnwantedChar(\$orf);
&DeleteUnwantedChar(\$fold);
if (!$orf || !$fold) {
print "You have to pass the feature_name and expression fold change for displaying the dataset and experiment list.",p;
return;
}
my $featObj = Feature->new(dbh=>$dbh,
feature_name=>$orf);
if (!$featObj) {
print "The feature_name $orf is not found in our database.",p;
return;
}
my $showNm = $featObj->locus_name;
if ($showNm) { $showNm .= "/"; }
$showNm .= $featObj->feature_name;
$showNm = a({-href=>$configUrl->dictyBaseCGIRoot."gene_page.pl?gene_name=".$featObj->feature_name}, $showNm);
my $arrayRef = Dataset->GetDatasetSampleBYfeatureNo(dbh=>$dbh,
feature_no=>$featObj->feature_no);
if (!@$arrayRef) {
print "No expression data found for feature_name $orf.",p;
return;
}
my $rows;
foreach my $rowRef (@$arrayRef) {
my ($dataset, $expt, $exprVal) = @$rowRef;
my ($thisfold, $decimal) = split(/\./, $self->exprFold($exprVal));
if ($decimal >= 5 && $thisfold >= 0) {
$thisfold++;
}
elsif ($decimal >= 5 && $thisfold < 0) {
$thisfold--;
}
if ($thisfold != $fold) { next; }
$rows .= Tr(td($dataset).td($expt));
}
my $text;
if ($fold > 0) {
$text = "increased ${fold}-fold";
}
elsif ($fold < 0) {
$fold =~ s/^-//;
$text = "decreased ${fold}-fold";
}
else { $text = "not changed"; }
print center(font({-size=>'+2'}, b("Experiment(s) with expression $text for $showNm"))),p;
print table({-align=>'center',
border=>1,
cellpadding=>3},
Tr({-bgcolor=>'#a4abc2'},
th("Dataset").
th("Experiment")).
$rows),p;
}
########################################################################
sub showHistogramForGene {
########################################################################
my ($self) = @_;
my $orf = param('orf');
&DeleteUnwantedChar(\$orf);
if (!$orf) {
print "You have to pass the feature_name for displaying the histogram",p;
return;
}
my $featObj = Feature->new(dbh=>$dbh,
feature_name=>$orf);
if (!$featObj) {
print "The feature_name $orf is not found in our database.",p;
return;
}
my $arrayRef = Dataset->GetExprValBYfeatureNo(dbh=>$dbh,
feature_no=>$featObj->feature_no);
if (!@$arrayRef) {
print "No expression data found for feature_name $orf.",p;
return;
}
my %count4fold;
foreach my $rowRef (@$arrayRef) {
my ($exprVal) = @$rowRef;
my ($fold, $decimal) = split(/\./, $self->exprFold($exprVal));
if ($decimal >= 5 && $fold >= 0) {
$fold++;
}
elsif ($decimal >= 5 && $fold < 0) {
$fold--;
}
$count4fold{$fold}++;
}
my ($maxCount, $minFold, $maxFold);
foreach my $fold (sort {$a<=>$b} keys %count4fold) {
if (!$maxCount || $maxCount < $count4fold{$fold}) {
$maxCount = $count4fold{$fold};
}
if (!$maxFold || $maxFold < $fold) {
$maxFold = $fold;
}
if (!$minFold || $minFold > $fold) {
$minFold = $fold;
}
}
my $showNm = $featObj->locus_name;
if ($showNm) { $showNm .= "/"; }
$showNm .=$featObj->feature_name;
my $border = 50;
my $width = ($maxFold - $minFold + 1)*15;
if ($width < 350) { $width = 350; }
my $height = 300;
### Create output image object
my $gd = CreateGD->new(width=>$width+2*$border,
height=>$height+2*$border);
print "";
my $gifDir = $configPath->tmpDir;
my $gifHttp = $configUrl->dictyBaseHtmlTmp;
my $gifname = "histogram.$$.gif";
open (OUT, ">".$gifDir.$gifname)||die "Can't create ".$gifDir.$gifname.":$!";
binmode OUT;
print OUT $gd->im->gif;
close OUT;
print center(font({-size=>'+2'}, b("Expression Histogram for ".a({-href=>$configUrl->dictyBaseCGIRoot."gene_page.pl?gene_name=".$featObj->feature_name}, $showNm)))),p;
# print center(img({-src=>$gifHttp.$gifname,
# -usemap=>'#histogramGif'})),p;
print ul(li("This graph shows you how many experiments ".a({-href=>$configUrl->dictyBaseCGIRoot."gene_page.pl?gene_name=".$featObj->feature_name}, $showNm)." mRNA expression changed by 2 fold, 4 fold, and etc.").
li("A negative number means expression is repressed. A positive
number means expression is induced.").
li("Click on the bars to see the list of experiments.")),p;
print center(img({-src=>$gifHttp.$gifname,
-usemap=>'#histogramGif'})),p;
}
########################################################################
sub drawTitle {
########################################################################
my ($self, $gd, $showNm, $width, $height, $border) = @_;
my $mapTitle = "Number of Experiments vs. Fold Change in $showNm";
my $nameX = $border + $width/2-length($mapTitle)*4;
my $nameY = 15;
$gd->im->string(gdLargeFont, $nameX, $nameY, $mapTitle,
$gd->black);
}
########################################################################
sub drawBorderAndBackground {
########################################################################
my ($self, $gd, $width, $height, $border) = @_;
$gd->im->filledRectangle($border+1, $border+1,
$width+$border-2, $height+$border-2,
$gd->lightGrey);
$gd->im->rectangle($border, $border, $width+$border-1,
$height+$border-1, $gd->maroon);
$gd->im->rectangle($border+1, $border+1,
$width+$border-2, $height+$border-2,
$gd->maroon);
}
########################################################################
sub drawXlabel {
########################################################################
my ($self, $gd, $minFold, $maxFold, $width,
$height, $border) = @_;
my $foldUnit = 2;
if ($maxFold - $minFold > 20) { $foldUnit = 5; }
elsif($maxFold - $minFold <= 6) { $foldUnit = 1; }
my $dx = $width*$foldUnit/($maxFold-$minFold+2*$foldUnit);
my $fold;
if ($minFold < 0) {
$fold = int($minFold/$foldUnit-1)*$foldUnit;
}
else {
$fold = int($minFold/$foldUnit)*$foldUnit;
}
my $xStart = 10;
my $pixelPerFold = $dx/$foldUnit;
my $xStartForMinFold = $xStart + ($minFold-$fold)*$pixelPerFold;
for (my $X = $border+$xStart; $X < $width+$border; $X += $dx) {
my $x = $X;
$gd->im->line($x, $height+$border-1, $x, $height+$border-5,
$gd->black);
if ($fold <= -10) { $x -= 6; }
elsif ($fold >= 0 && $fold < 10) { $x += 6; }
elsif ($fold > 10) { $x += 3; }
$gd->im->string(gdLargeFont, $x-10, $height+$border, $fold,
$gd->black);
$fold += $foldUnit;
}
my $xLabel = "Fold Change";
my $nameX = $border + $width/2-length($xLabel)*4;
my $nameY = $height + $border + 20;
$gd->im->string(gdLargeFont, $nameX, $nameY, $xLabel,
$gd->black);
return ($pixelPerFold, $xStartForMinFold);
}
########################################################################
sub drawYlabel {
########################################################################
my ($self, $gd, $maxCount, $width, $height, $border) = @_;
my $countUnit;
if ($maxCount > 200) { $countUnit = 50; }
if ($maxCount > 100) { $countUnit = 20; }
elsif ($maxCount > 50) { $countUnit = 10; }
elsif ($maxCount > 20) { $countUnit = 5; }
else { $countUnit = 2; }
my $dy = ($height-25)*$countUnit/$maxCount;
my $pixelPerCount = $dy/$countUnit;
my $count = 0;
for (my $Y = $height+$border; $Y >= $border; $Y -= $dy) {
my $y = $Y;
if ($count != 0) {
$gd->im->line($border+1, $y, $border+$width-1, $y,
$gd->darkGrey);
}
if ($count < 10) { $y -= 12; }
elsif ($count < 100) { $y -= 6; }
$gd->im->stringUp(gdLargeFont, $border-15, $y+12, $count,
$gd->black);
$count += $countUnit;
}
my $yLabel = "Number of Experiments";
my $nameY = ($height+2*$border)/2+length($yLabel)*4;
my $nameX = 10;
$gd->im->stringUp(gdLargeFont, $nameX, $nameY, $yLabel,
$gd->black);
return $pixelPerCount;
}
########################################################################
sub drawBars {
########################################################################
my ($self, $gd, $pixelPerFold, $xStartForMinFold, $minFold,
$pixelPerCount, $count4foldHashRef, $height, $border,
$orf) = @_;
foreach my $fold (keys %$count4foldHashRef) {
my $x = $border + $xStartForMinFold +
($fold-$minFold)*$pixelPerFold;
my $x1 = $x - 4;
my $x2 = $x1 + 8;
my $y1 = $height + $border -
$$count4foldHashRef{$fold}*$pixelPerCount;
my $y2 = $height+$border-3;
if ($y1 >= $y2) { $y1 -= 3; }
my $linkUrl = url."?orf=$orf&fold=$fold";
MapUtil->DrawBar(gd=>$gd,
barColor=>$gd->maroon,
numX1=>$x1,
numX2=>$x2,
numY=>$y1,
linkUrl=>$linkUrl,
barHeight=>$y2-$y1+1);
}
}
########################################################################
sub showRegulatorList {
########################################################################
my ($self) = @_;
if (!param('id') || !param('orf') || !param('dataset')) {
print "You have to pass id, orf name, and dataset name in order to show the regulator list.",p;
return;
}
my $id = param('id');
my $orf = param('orf');
my $dataset = param('dataset');
&DeleteUnwantedChar(\$id);
&DeleteUnwantedChar(\$orf);
&DeleteUnwantedChar(\$dataset);
my $tmpfile = $configPath->tmpDir."regulatorFor$orf.$dataset.$id";
open(TMP, "$tmpfile") ||
die "Can't open '$tmpfile' for reading:$!";
my @featNm;
while() {
chomp;
@featNm = split(/:/);
last;
}
close(TMP);
my $datasetObj = Dataset->new(dbh=>$dbh,
dataset_name=>$dataset);
my $datasetTitle;
if ($datasetObj) {
$datasetTitle = $datasetObj->title;
}
else {
$datasetTitle = $dataset;
}
my $datasetNo = $datasetObj->dataset_no;
my $list;
foreach my $featNm (@featNm) {
my $featObj = Feature->new(dbh=>$dbh,
feature_name=>$featNm);
my $showNm;
if ($featObj->locus_name) {
$showNm = $featObj->locus_name."/";
}
$showNm .= $featNm;
my $regulatorUrl = $self->getRegulatorModuleUrl($dataset, $datasetNo,
$featNm, $featObj->feature_no);
$list .= li(a({-href=>$regulatorUrl,
-target=>'infowin'},
$showNm));
}
print b(font({-color=>'red'}, "$orf")." in ".font({-color=>'red'}, $datasetTitle)." dataset is regulated by following genes:"),p;
print ul($list),p ;
}
########################################################################
sub showRegulationModuleList {
########################################################################
my ($self) = @_;
if (!param('orf') || !param('dataset')) {
print "You have to orf name and dataset name in order to show the regulation module list.",p;
return;
}
my $orf = param('orf');
my $dataset = param('dataset');
&DeleteUnwantedChar(\$orf);
&DeleteUnwantedChar(\$dataset);
my $datasetObj = Dataset->new(dbh=>$dbh,
dataset_name=>$dataset);
my $datasetTitle;
if ($datasetObj) {
$datasetTitle = $datasetObj->title;
}
else {
$datasetTitle = $dataset;
}
my $datasetNo = $datasetObj->dataset_no;
my $featObj = Feature->new(dbh=>$dbh,
feature_name=>$orf);
if (!$featObj) {
print "The feature_name = '$orf' is not found in database",p;
return;
}
my $showNm;
if ($featObj->locus_name) {
$showNm = $featObj->locus_name."/";
}
$showNm .= $featObj->feature_name;
my $regulatorModuleArrayRef =
Dataset->RegulatorModuleArrayRef(dbh=>$dbh,
dataset_no=>$datasetNo,
feature_no=>$featObj->feature_no);
my $list;
foreach my $rowRef (@$regulatorModuleArrayRef) {
my ($module) = @$rowRef;
my $moduleShowNm = $module;
$module =~ s/^Module ([0-9]+)$/cluster_${1}\.html/i;
$list .= li(a({-href=>$configUrl->wineServerRoot."Dictyostelium/exp_modules/$dataset/$module",
-target=>'infowin'},
$moduleShowNm));
}
print b(font({-color=>'red'}, $showNm)." in ".font({-color=>'red'}, $datasetTitle)." dataset belongs to following regulation modules:"),p;
print ul($list),p ;
}
########################################################################
sub showSimilarResult {
########################################################################
my ($self) = @_;
my $dataset = param('dataset');
my $orf = param('orf');
&DeleteUnwantedChar(\$dataset);
&DeleteUnwantedChar(\$orf);
my $datasetObj = Dataset->new(dbh=>$dbh,
dataset_name=>$dataset);
$dataset = $datasetObj->dataset_name;
if (!$dataset || !$orf) {
print "You have to pass dataset_name and feature_name for displaying similarly expressed genes.",p;
return;
}
my $gene = $orf;
my $seqObj = SeqParamTranslator->new(dbh=>$dbh,
query=>$orf);
if (!$seqObj->error && $seqObj->featureObject) {
$orf = $seqObj->featureObject->feature_name;
}
else {
print "You have to pass dataset_name and feature_name or physically mapped gene name for displaying similarly expressed genes.",p;
return;
}
my $tmpfile;
@orf = $self->getSimilarGenes($dataset, $orf);
my $downloadUrl = $configUrl->dictyBaseHtmlTmp.$tmpfile;
my @newORF;
foreach my $orf (@orf) {
my $featObj = Feature->new(dbh=>$dbh,
feature_name=>$orf);
if (!$featObj) { next; }
$orf = $featObj->feature_name;
$featNo4featNm{$orf} = $featObj->feature_no;
$gene4featNm{$orf} = $featObj->locus_name;
push(@newORF, $orf);
}
if (!@newORF) {
print "No similarly expressed gene found for $gene.";
return;
}
my ($genes, $expts) = $self->createColorStrips($dataset);
my $width = $expts * 16;
my $height = 16;
my $rows;
my $bgcolor = "white";
my %goTerms4orf;
foreach my $orf (@newORF) {
my $gif = $configUrl->dictyBaseHtmlTmp."$orf.$dataset.gif";
my $dictyBase = dictyBaseObject->new(dbh=>$dbh,
query=>$orf);
my $gene = $gene4featNm{$orf} || '-';
$rows .= Tr({-bgcolor=>$bgcolor},
td(a({-href=>$locusUrl.$orf}, $orf)).
td($gene).
td(a({-href=>url."?dataset=$dataset&orf=$orf&type=similar"},
img({-alt=>'GIF',
-width=>$width,
-height=>'16',
-src=>$gif}))).
td(font({-size=>'-1'}, $dictyBase->process)).
td(font({-size=>'-1'}, $dictyBase->function)).
td(font({-size=>'-1'}, $dictyBase->component)));
$goTerms4orf{"\U$orf"} =
$dictyBase->process."\t".$dictyBase->function."\t".$dictyBase->component;
if ($bgcolor eq "white") { $bgcolor = "#d8d8d8"; }
else { $bgcolor = "white"; }
}
my ($datasetTitle, $link) = $self->datasetsTable($dataset);
print table({-width=>'100%'},
Tr(td({-bgcolor=>'#a4abc2'},
font({-size=>'+2'}, b("Similarly Expressed Genes: $datasetTitle"))." ".$link))),p;
print table(Tr(td(b("Scale"))).
Tr(td(img({-border=>0,
-valign=>'bottom',
-width=>400,
-src=>$configUrl->dictyBaseImages."scale.1.5.gif"})))),p;
print b("Click on a color strip to see 20 genes expressed similarly to that gene"),p;
print b("Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene"),p;
print table(Tr(th({-bgcolor=>'#b7d8e4'}, "ORF").
th({-bgcolor=>'#b7d8e4'}, "Gene").
th({-bgcolor=>'#b7d8e4'},
img({-src=>$configUrl->dictyBaseImages."$dataset.gif"})).
th({-bgcolor=>'#b7d8e4'}, "Go Process term").
th({-bgcolor=>'#b7d8e4'}, "Go Function term").
th({-bgcolor=>'#b7d8e4'}, "Go Component term")).
$rows);
if (@orf > 2) {
$self->manageGeneList(\@orf, $dataset, \%goTerms4orf);
}
# $self->createDownLoadLink($dataset, \%goTerms4orf);
}
########################################################################
sub showEnlargeResult {
########################################################################
my ($self) = @_;
my $dataset = param('dataset');
my $id = param('id');
my $expts = param('expts');
my $orf = param('orf');
&DeleteUnwantedChar(\$dataset);
&DeleteUnwantedChar(\$id);
&DeleteUnwantedChar(\$expts);
&DeleteUnwantedChar(\$orf);
my $width;
if ($expts) { $width = $expts * 16; }
else { $width = 125; }
my $height = 16;
if (!$dataset || (!$id && !$orf)) {
print "You have to pass dataset_name and feature_name or gene list file id for displaying the big result picture.",p;
return;
}
my @loci;
if ($id) {
my $tmpfile = $configPath->tmpDir."more.".$id;
open(IN, $tmpfile) || die "Can't open '$tmpfile' for reading:$!";
while() {
chomp;
my @gene = split(/\:/);
push(@loci, @gene);
}
close(IN);
}
else {
@loci = $orf;
}
my ($datasetTitle, $link) = $self->datasetsTable($dataset);
print table({-width=>'100%'},
Tr(td({-bgcolor=>'#a4abc2'},
font({-size=>'+2'}, b($datasetTitle))." ".$link))),p;
if (param('showGeneNum')) {
$maxDisplayNum = param('showGeneNum');
}
my $rows;
my $bgcolor = "white";
my %lociHash;
my %goTerms4orf;
my @noExpressedLoci;
my $count;
my @pearsonORF;
foreach my $locus (@loci) {
my $dictyBase = dictyBaseObject->new(dbh=>$dbh,
query=>$locus);
my $orf = $dictyBase->featureName;
my $gene = $dictyBase->locusName || "-";
if (!$orf && $gene eq "-") { ##### one locus for more than one orf
##### or the given name is std gene name
##### and is an alias
my $locusObj = Locus->new(dbh=>$dbh,
locus_name=>$locus);
if (!$locusObj) { next; }
my @featNm = split(/\|/, $locusObj->featureNameList);
push(@orf, @featNm);
foreach my $featNm (@featNm) {
$dictyBase = dictyBaseObject->new(dbh=>$dbh,
query=>$featNm);
$orf = $featNm;
$gene = $dictyBase->locusName || "-";
goto ROW;
}
}
else {
push(@orf, $orf);
goto ROW;
}
ROW:{
$goTerms4orf{"\U$orf"} =
$dictyBase->process."\t".$dictyBase->function."\t".$dictyBase->component;
$lociHash{"\U$orf"} = $gene;
if (! -e $configPath->tmpDir."$orf.$dataset.gif") {
push(@noExpressedLoci, $locus);
}
else {
$count++;
if ($count > $maxDisplayNum) { next; }
push(@pearsonORF, $orf);
my $gif = $configUrl->dictyBaseHtmlTmp."$orf.$dataset.gif";
$rows .= Tr({-bgcolor=>$bgcolor},
td(a({-href=>$locusUrl.$orf}, $orf)).
td($gene).
td(img({-alt=>'GIF',
-width=>$width,
-height=>'16',
-src=>$gif})).
td(font({-size=>'-1'}, $dictyBase->process)).
td(font({-size=>'-1'}, $dictyBase->function)).
td(font({-size=>'-1'}, $dictyBase->component)));
if ($bgcolor eq "white") { $bgcolor = "#d8d8d8"; }
else { $bgcolor = "white"; }
}
}
}
if ($count == 1) {
print b("There are no genes in this dataset with a Pearson correlation > 0.8 to the query gene."),p;
}
if (param('showGeneNum')) {
$self->manageGeneList(\@orf, $dataset, \%goTerms4orf);
print p;
}
print table(Tr(th({-valign=>'bottom',
-bgcolor=>'#b7d8e4'}, "ORF").
th({-valign=>'bottom',
-bgcolor=>'#b7d8e4'}, "Gene").
th({-valign=>'bottom',
-bgcolor=>'#b7d8e4'},
img({-src=>$configUrl->dictyBaseImages."$dataset.gif"})).
th({-valign=>'bottom',
-bgcolor=>'#b7d8e4'}, "Go Process term").
th({-valign=>'bottom',
-bgcolor=>'#b7d8e4'}, "Go Function term").
th({-valign=>'bottom',
-bgcolor=>'#b7d8e4'}, "Go Component term")).
$rows);
# if (@noExpressedLoci) {
# print p, b("There is no expression data available in $datasetTitle for following genes:"),p;
# foreach my $locus (@noExpressedLoci) {
# print li(a({-href=>$locusUrl.$locus}, $locus));
# }
# }
if (@loci > 2 && !param('showGeneNum')) {
$self->manageGeneList(\@orf, $dataset, \%goTerms4orf);
if ($id && $count > $maxDisplayNum) {
print center(b(a({-href=>url."?dataset=$dataset&id=$id&type=enlarge&expts=$expts&showGeneNum=100"},
"Show More Genes"))),p;
}
$self->showCorrelationGraph($dataset, \%lociHash, \@pearsonORF,
$datasetTitle);
}
$self->lineSeparator;
}
########################################################################
sub showGraph {
########################################################################
my ($self) = @_;
my $dataset = param('dataset');
my $id = param('id');
my $orf = param('orf');
my @orfs = param('orfs');
&DeleteUnwantedChar(\$dataset);
&DeleteUnwantedChar(\$id);
&DeleteUnwantedChar(\$orf);
if (!$dataset || (!$id && !$orf)) {
print "You have to pass dataset_name and feature_name or gene list file id for displaying the graph.",p;
return;
}
my @loci;
if ($id) {
my $tmpfile = $configPath->tmpDir."more.".param('id');
open(IN, $tmpfile) || die "Can't open '$tmpfile' for reading:$!";
while() {
chomp;
@loci = split(/\:/, $_);
last;
}
close(IN);
}
else { @loci = $orf; }
my ($datasetTitle, $link) = $self->datasetsTable($dataset);
print table({-width=>'100%'},
Tr(td({-bgcolor=>'#a4abc2'},
font({-size=>'+2'}, b("Expression Graph: $datasetTitle"))." ".$link))),p;
my %lociHash;
my %goTerms4orf;
# my @orf;
my $count;
foreach my $gene (@loci) {
$count++;
if (@loci > 50 && $count%20 == 0) {
my $count1 = $count - 19;
print "Retrieving info for 'Download Data' option, gene No. $count1 to $count, please wait...",br;
}
my $dictyBase = dictyBaseObject->new(dbh=>$dbh,
query=>$gene);
my $orf = $dictyBase->featureName;
my $gene = $dictyBase->locusName || "-";
push(@orf, $orf);
$goTerms4orf{"\U$orf"} =
$dictyBase->process."\t".$dictyBase->function."\t".$dictyBase->component;
$lociHash{"\U$orf"} = $gene;
}
my $showPopup;
if (@orf > $maxDisplayNum) {
$showPopup = $self->showPopupForGeneList($id, $dataset, \@orf);
}
if (!@orfs) { @orfs = @orf; }
$self->drawGraph($dataset, \%lociHash, \@orfs,
$datasetTitle, $showPopup);
if (@orf >= 2) {
$self->manageGeneList(\@orf, $dataset, \%goTerms4orf);
}
$self->lineSeparator;
}
########################################################################
sub showPopupForGeneList {
########################################################################
my ($self, $id, $dataset, $orfArrayRef) = @_;
return start_form.
table({-align=>'center'},
Tr(td({-nowrap=>'1',
-valign=>'top'},
b("Choose genes from following list to redraw the graph:"),
br."(do not choose more than $maxDisplayNum genes)")).
Tr(td(popup_menu(-name=>'orfs',
-values=>$orfArrayRef,
-multiple=>'yes',
-size=>'10').p.
"Select or unselect multiple gene names".br.
"by pressing the Control (PC) or Command".br.
"(Mac) key while clicking.".p)).
Tr(td(hidden(-name=>'type',
-value=>'graph').
hidden(-name=>'id',
-value=>$id).
hidden(-name=>'dataset',
-value=>$dataset).
submit(-name=>'Redraw graph')))).
end_form;
}
########################################################################
sub drawGraph {
########################################################################
my ($self, $dataset, $lociHashRef, $orfArrayRef, $datasetTitle,
$showPopup) = @_;
my $count;
my $sampleUnit;
my $minExprVal = 0;
my $maxExprVal = 0;
my @data;
my @expt;
foreach my $orf (@$orfArrayRef) {
if (!$orf) { next; }
my $ecPointArrayRef = Dataset->GetECpointArrayRef(dbh=>$dbh,
feature_name=>$orf,
dataset_name=>$dataset);
$count++;
if ($count > $maxDisplayNum) { last; }
my @row = ($orf);
foreach my $rowRef (@$ecPointArrayRef) {
my ($expt, $unit, $exprVal) = @$rowRef;
if ($count == 1) {
if (!$sampleUnit) { $sampleUnit = $unit; }
push(@expt, $expt);
}
if ($exprVal > $maxExprVal) { $maxExprVal = $exprVal; }
if ($exprVal < $minExprVal) { $minExprVal = $exprVal; }
push(@row, $exprVal);
}
push(@data, \@row);
print p;
}
my $width = 350;
my $height = 350;
my $wRatio = ($width-40)/$expt[$#expt];
my $hRatio = ($height-100)/($maxExprVal-$minExprVal);
my $border = 60;
my $legendRow = scalar(@data)/3;
if (scalar(@data)%3 != 0) { $legendRow++; }
my $bottomH = $legendRow*20;
if (@data == 1) { undef $bottomH; }
print "";
my $gifDir = $configPath->tmpDir;
my $gifHttp = $configUrl->dictyBaseHtmlTmp;
my $gifname = "ecGraph.$$.gif";
open (OUT, ">".$gifDir.$gifname)||die "Can't create ".$gifDir.$gifname.":$!";
binmode OUT;
print OUT $gd->im->gif;
close OUT;
print table({-align=>'center'},
Tr(td({-valign=>'top'},
$showPopup).
td({-valign=>'top'},
img({-src=>$gifHttp.$gifname,
-usemap=>'#graph'})))),p,p;
}
########################################################################
sub setLineColor {
########################################################################
my ($self, $gd, $lineColorRef) = @_;
@$lineColorRef = ($gd->blue,
$gd->magenta,
$gd->orange,
$gd->maroon,
$gd->darkGreen,
$gd->blue2,
$gd->sagecolor1,
$gd->sagecolor2,
$gd->sagecolor3,
$gd->sagecolor4,
$gd->yellow,
$gd->magenta2,
$gd->red3,
$gd->yellow3,
$gd->lightBlue,
$gd->green5,
$gd->blue3,
$gd->blue4,
$gd->red2,
$gd->green3);
}
########################################################################
sub showPearsonCorrelation {
########################################################################
my ($self) = @_;
my $dataset = param('dataset');
my $id = param('id');
&DeleteUnwantedChar(\$dataset);
&DeleteUnwantedChar(\$id);
if (!$dataset || !$id) {
print "You have to pass dataset_name and gene list file id for displaying the Pearson correlation result.",p;
return;
}
my $tmpfile = $configPath->tmpDir."more.".param('id');
open(IN, $tmpfile) || die "Can't open '$tmpfile' for reading:$!";
my @loci;
while() {
chomp;
@loci = split(/\:/, $_);
last;
}
close(IN);
my ($datasetTitle, $link) = $self->datasetsTable($dataset);
my %lociHash;
my @orf;
foreach my $gene (@loci) {
my $dictyBase = dictyBaseObject->new(dbh=>$dbh,
query=>$gene);
my $orf = $dictyBase->featureName;
my $gene = $dictyBase->locusName || "-";
push(@orf, $orf);
$lociHash{"\U$orf"} = $gene;
}
$self->showCorrelationGraph($dataset, \%lociHash, \@orf,
$datasetTitle);
$self->lineSeparator;
}
########################################################################
sub showCorrelationGraph {
########################################################################
my ($self, $dataset, $lociHashRef, $orfArrayRef, $datasetTitle)
= @_;
my $pcl = $configPath->dataDir4web."dictyBase/$dataset/$dataset.pcl";
open(IN, $pcl) || die "Can't open '$pcl' for reading:$!";
my $pclTmp = $configPath->tmpDir."$$.pcl";
open(OUT, ">$pclTmp") || die "Can't open '$pclTmp' for writing:$!";
my $i;
while() {
my ($orf, $others) = split(/\t/);
$i++;
if ($i <= 2 || $$lociHashRef{"\U$orf"}) {
print OUT;
}
}
close(IN);
close(OUT);
my $stdCor = $configPath->tmpDir."$$.stdCor";
my $tmpfile = $configPath->tmpDir."$$.tmp";
my $correlations = $configPath->binDir."correlations";
system("$correlations -f $pclTmp -cutoff 0.4 > $tmpfile");
open(IN, $stdCor) || die "Can't open '$stdCor' for reading:$!";
$self->lineSeparator;
print table({-width=>'100%'},
Tr(td({-bgcolor=>'#a4abc2'},
font({-size=>'+2'}, b("Pearson Correlations for $datasetTitle")))));
print "The Pearson correlation is a statistical measure of how similar the expression of two gene products is. Pearson = 1.0 represents a perfect correlation.",p;
print "Click on a square to use GO Term Finder to find common processes, functions, or localizations for the two genes.", p,p;
if (@$orfArrayRef >= 50) {
print p, center("Graphic is not displayed if the gene list has more than 50 genes.");
print p, center(a({-href=>$configUrl->dictyBaseHtmlTmp."$$.stdCor",
-target=>'infowin'},
"Download Pearson Correlation Data")),p;
return;
}
my %Pearson;
while() {
chomp;
my @list = split(/\t/);
my $orf1 = shift (@list);
$orf1 = "\U$orf1";
if (!@list) { next; }
for (my $i = 0; $i < @list; $i += 2) {
my $orf2 = "\U$list[$i]";
$Pearson{$orf1.":".$orf2} = $list[$i+1];
$Pearson{$orf2.":".$orf1} = $list[$i+1];
}
}
close(IN);
my ($blockH, $blockW);
if (scalar(@$orfArrayRef) > 40) {
$blockH = 10;
$blockW = 10;
}
elsif (scalar(@$orfArrayRef) > 20) {
$blockH = 15;
$blockW = 15;
}
else {
$blockH = 25;
$blockW = 25;
}
my $border = 65;
if (@$orfArrayRef <= 3) {
$border += 20;
}
my $width = (scalar(@$orfArrayRef) + 2 )*$blockW;
my $height = (scalar(@$orfArrayRef) + 1 )*$blockH;
print "";
my $gifDir = $configPath->tmpDir;
my $gifHttp = $configUrl->dictyBaseHtmlTmp;
my $gifname = "correlation.$$.gif";
open (OUT, ">".$gifDir.$gifname)||die "Can't create ".$gifDir.$gifname.":$!";
binmode OUT;
print OUT $gd->im->gif;
close OUT;
print center(img({-src=>$gifHttp.$gifname,
-usemap=>'pearsonMap'})),p,p;
}
########################################################################
sub sortAndShowResult {
########################################################################
my ($self) = @_;
$loci = param('loci');
@dataset = param('dataset');
$sortBy = param('sortBy');
$exprtype = param('exprtype');
$fold = param('fold');
if ($sortBy =~ /- Sort genes in datasets -/i) { undef $sortBy; }
if ($exprtype =~ /-Select/i) { undef $exprtype; }
if (param('option1')) {
$self->showResultForOption1;
}
elsif (param('option2')) {
$self->showResultForOption2;
}
else {
$self->showResultForOption3;
}
}
########################################################################
sub showDownloadList {
########################################################################
my ($self) = @_;
print b("The download files are under construction."),p;
### show download file list here
}
########################################################################
sub printNoDataResultForDataset {
########################################################################
my ($self, $dataset) = @_;
print hr({-size=>1,
-width=>'100%'});
my $datasetObj = Dataset->new(dbh=>$dbh,
dataset_name=>$dataset);
my $arrayRef = $datasetObj->getNoDataFeatureArrayRef;
my $hits = scalar(@$arrayRef);
my ($datasetTitle, $link) = $self->datasetsTable($dataset);
print p, b($datasetTitle." ".$link),p;
print "$hits ORFs are found with No Expression or No Data in $datasetTitle.",p;
my $tmpfile = "NoDataFor$dataset.$$.xls";
open(TMP, ">".$configPath->tmpDir.$tmpfile) ||
die "Can't open '".$configPath->tmpDir.$tmpfile."' for writing:$!";
foreach my $rowRef (@$arrayRef) {
my ($featNm, $locusNm) = @$rowRef;
print TMP "$featNm\t$locusNm\n";
}
close(TMP);
print b(a({-href=>$configUrl->dictyBaseHtmlTmp.$tmpfile,
-target=>'infowin'},
"Download Gene List with No Expression/No Data")),p;
}
########################################################################
sub printNoDataResultForOrf {
########################################################################
my ($self, $orf) = @_;
print hr({-size=>1,
-width=>'100%'}), p;
my $arrayRef =
Dataset->GetDatasetArrayRefBYfeatureNo(dbh=>$dbh,
feature_no=>$featNo4featNm{$orf});
my $showNm;
if ($gene4featNm{$orf}) {
$showNm = $gene4featNm{$orf}."/";
}
$showNm .= $orf;
print b(a({-href=>$configUrl->dictyBaseCGIRoot."gene_page.pl?gene_name=$orf",
-target=>'infowin'},
$showNm)), p;
if (!@$arrayRef) {
print "No dataset is found with 'No Expression/No Data' for $showNm.",p;
}
my $datasetList;
foreach my $rowRef (@$arrayRef) {
my ($dataset) = @$rowRef;
my ($datasetTitle, $link) = $self->datasetsTable($dataset);
$datasetList .= li($datasetTitle." ".$link);
}
my $desc;
if (@$arrayRef == 1) { $desc = "One dataset "; }
else { $desc = scalar(@$arrayRef)." datasets "; }
$desc .= "found with 'No Expression/No Data' for $showNm";
print b($desc),p, ul($datasetList),p;
}
########################################################################
sub getResultForDataset {
########################################################################
my ($self, $dataset, $id) = @_;
if ($id) {
$self->setGeneList($dataset, $id);
}
if (!$id) { $id = $$; }
my $datasetObj = Dataset->new(dbh=>$dbh,
dataset_name=>$dataset);
if (!$datasetObj) { return; }
my $datasetNo = $datasetObj->dataset_no;
foreach my $featNm (keys %featNo4featNm) {
if (!$featNo4featNm{$featNm}) {
# print $featNm, br;
next;
}
my $max = Dataset->MaxExprValBYdatasetNofeatureNo(dbh=>$dbh,
dataset_no=>$datasetNo,
feature_no=>$featNo4featNm{$featNm});
my $min = Dataset->MinExprValBYdatasetNofeatureNo(dbh=>$dbh,
dataset_no=>$datasetNo,
feature_no=>$featNo4featNm{$featNm});
if (!$max && !$min) { next; }
if ($max =~ /^[0\.]+$/) {
$maxExprVal4featNm{$featNm} = 1;
}
elsif ($max > 0) {
$maxExprVal4featNm{$featNm} = $self->exprFold($max);
}
elsif ($max) {
$maxExprVal4featNm{$featNm} = -1000;
}
else { next ; }
if ($min =~ /^[0\.]+$/) {
$minExprVal4featNm{$featNm} = 1;
}
elsif ($min < 0) {
$minExprVal4featNm{$featNm} = $self->exprFold($min);
}
elsif ($min) {
$minExprVal4featNm{$featNm} = 1000;
}
}
my ($genes, $expts) =
$self->createColorStrips($dataset);
my ($rows, $geneNum);
my @featNm;
if ($sortBy =~ /by ORF name/i) {
@featNm = sort (keys %maxExprVal4featNm);
}
elsif ($sortBy =~ /Greatest to least Max Increase/i) {
@featNm = sort ({$maxExprVal4featNm{$b} <=> $maxExprVal4featNm{$a}} keys %maxExprVal4featNm);
}
elsif ($sortBy =~ /least to greatest Max Increase/i) {
@featNm = sort ({$maxExprVal4featNm{$a} <=> $maxExprVal4featNm{$b}} keys %maxExprVal4featNm);
}
elsif ($sortBy =~ /Greatest to least Max Decrease/i) {
@featNm = sort ({$minExprVal4featNm{$a} <=> $minExprVal4featNm{$b}} keys %maxExprVal4featNm);
}
elsif ($sortBy =~ /least to greatest Max Decrease/i) {
@featNm = sort ({$minExprVal4featNm{$b} <=> $minExprVal4featNm{$a}} keys %maxExprVal4featNm);
}
else { @featNm = @orf; }
my $showLongList;
if (@featNm > $maxDisplayNum && $maxDisplayNum < 100) {
$showLongList++;
}
my $tmpfile = "$dataset.$id.tmp";
my $downloadFile = $configPath->tmpDir.$tmpfile;
open(OUT, ">$downloadFile") ||
die "Can't open '$downloadFile' for writing:$!";
print OUT "ORF\tGene\tMax_Increase\tMax_Decrease\n";
$geneNum4dataset{$dataset} = scalar(@featNm);
my $bgcolor = 'white';
foreach my $featNm (@featNm) {
if (!$featNo4featNm{$featNm}) {
next;
}
if (!$minExprVal4featNm{$featNm} && !$maxExprVal4featNm{$featNm}) {
$self->{'_noData'}{$dataset} .= ":".$featNm;
next;
}
my $gene = $gene4featNm{$featNm} || br;
my $max = $maxExprVal4featNm{$featNm};
my $min = $minExprVal4featNm{$featNm};
if ($max == -1000) { $max = "-"; }
if ($min == 1000) { $min = "-"; }
print OUT "$featNm\t$gene4featNm{$featNm}\t$max\t$min\n";
if ($geneNum >= $maxDisplayNum) {
next;
}
$geneNum++;
my $linkNm = a({-href=>$locusUrl.$featNm,
-target=>'infowin'},
$featNm);
my $regulatorUrl =
$self->getRegulatorModuleUrl($dataset,
$datasetNo,
$featNm,
$featNo4featNm{$featNm});
my $regulator;
if ($regulatorUrl) {
$regulator = a({-href=>$regulatorUrl,
-target=>'infowin'},
img({-border=>'0',
-width=>'32',
-height=>'20',
-alt=>'regulator',
-src=>$configUrl->dictyBaseImages."reg.PNG"}));
}
else { $regulator = br; }
my $regulatorArrayRef = Dataset->GetRegulatorArrayRef(dbh=>$dbh,
dataset_no=>$datasetNo,
feature_no=>$featNo4featNm{$featNm});
my $regulatedBy;
my $regulatorList;
my $count;
foreach my $rowRef (@$regulatorArrayRef) {
my ($orfname) = @$rowRef;
if ($regulatorList) { $regulatorList .= ":"; }
$regulatorList .= $orfname;
$count++;
if ($count > 2) { next; }
if (!$regulatedBy) {
my $featObj = Feature->new(dbh=>$dbh,
feature_name=>$orfname);
my $regulatorUrl =
$self->getRegulatorModuleUrl($dataset,
$datasetNo,
$orfname,
$featObj->feature_no);
my $regulatorShowNm;
if ($featObj->locus_name) {
$regulatorShowNm = $featObj->locus_name."/";
}
$regulatorShowNm .= $orfname;
$regulatedBy = a({-href=>$regulatorUrl,
-target=>'infowin'},
$regulatorShowNm);
}
else {
$regulatedBy .= "+".
a({-href=>url."?id=$id&orf=$featNm&dataset=$dataset&type=regulatedBy",
-target=>'infowin'},
"More");
}
}
if (!$regulatedBy) { $regulatedBy = br; }
if (@$regulatorArrayRef >= 2) {
my $tmpfile = $configPath->tmpDir."regulatorFor$featNm.$dataset.$id";
open(TMP, ">$tmpfile") || die "Can't open '$tmpfile' for writing:$!";
print TMP $regulatorList, "\n";
close(TMP);
}
my @similarGenes = $self->getSimilarGenes($dataset, $featNm);
my $similar;
if (@similarGenes) {
$similar = a({-href=>url."?orf=$featNm&dataset=$dataset&type=similar",
-target=>'infowin'},
img({-border=>'0',
-size=>'10',
-alt=>'similar genes',
-src=>$configUrl->dictyBaseImages."rd_ball.PNG"}));
}
else { $similar = br; }
$rows .= Tr({-bgcolor=>$bgcolor},
td($linkNm).
td($gene).
td($max).
td($min).
td({-align=>'center'},
a({-href=>url."?orf=$featNm&type=histogram",
-target=>'infowin'},
img({-border=>'0',
-size=>'10',
-alt=>'Histogram',
-src=>$configUrl->dictyBaseImages."cy_ball.gif"}))).
td({-align=>'center'},
img({-border=>'0',
-width=>'55',
-height=>'8',
-alt=>'GIF',
-src=>$configUrl->dictyBaseHtmlTmp.$featNm.".".$dataset.".gif"})).
td({-align=>'center'},
$similar).
td({-align=>'center'},
$regulator).
td($regulatedBy));
# td({-align=>'center'},
# a({-href=>$configUrl->dictyBaseCGIRoot."dictyBase/geneXplorer/geneXplorer.pl?dataset=$dataset&genes=$genes&expts=$expts",
# -target=>'infowin'},
# img({-border=>'0',
# -size=>'10',
# -alt=>'clustered',
# -src=>$configUrl->dictyBaseImages."bl_ball.gif"}))).
if ($bgcolor eq "white") {
$bgcolor = '#d8d8d8';
}
else { $bgcolor = 'white'; }
}
close(OUT);
my $rowspan= $geneNum + 2;
my ($graph, $pearson, $golink);
if ($datasetObj->hasECpoint && !param('showGeneNum')) {
$graph = th("Expression Graph".br.
a({-href=>url."?id=$id&dataset=$dataset&type=graph",
-target=>'infowin'},
img({-width=>30,
-border=>0,
-alt=>'graph',
-src=>$configUrl->dictyBaseImages."graph2.gif"})));
}
my $downloadUrl = $configUrl->dictyBaseHtmlTmp.$tmpfile;
my $downloadLink = b(a({-href=>$downloadUrl,
-target=>'infowin'},
"Download Data")).br.br.br;
if (@featNm >= 2 && !param('showGeneNum')) {
$pearson = th(" ").
th("Pearson Correlation".br.
a({-href=>url."?id=$id&dataset=$dataset&type=Pearson",
-target=>'infowin'},
img({-width=>35,
-border=>0,
-alt=>'Pearson Correlations',
-src=>$configUrl->dictyBaseImages."correlation.PNG"})));
$golink = th("Analyze Gene List with:".br.blockquote($self->golinks(\@featNm, $dataset, $downloadLink)));
undef $downloadLink;
}
else { $downloadLink = br." ".$downloadLink; }
if ($showLongList) {
#### To force it to overwrite the old dataset list
param('dataset', $dataset);
if (param('submit1') || param('option') =~ /option1/i) {
#### To force it to overwrite the old locus list
param('loci', $loci);
$downloadLink .=
start_form.
hidden(-name=>'loci',
-value=>$loci).
hidden(-name=>'dataset',
-value=>$dataset).
hidden(-name=>'sortBy',
-value=>$sortBy).
hidden(-name=>'showGeneNum',
-value=>'100').
hidden(-name=>'option',
-value=>'option1').
submit(-name=>'submit',
-value=>'Show More Genes').
end_form;
}
else {
#### To force it to overwrite the old value
param('showGeneNum', '100');
$downloadLink .=
start_form.
hidden(-name=>'showGeneNum',
-value=>'100').
hidden(-name=>'dataset',
-value=>$dataset).
hidden(-name=>'exprtype',
-value=>$exprtype).
hidden(-name=>'fold',
-value=>$fold).
hidden(-name=>'sortBy',
-value=>$sortBy).
hidden(-name=>'option',
-value=>'option3').
submit(-name=>'submit',
-value=>'Show More Genes').
end_form;
param('showGeneNum', '');
}
}
undef %maxExprVal4featNm;
undef %minExprVal4featNm;
my ($datasetTitle, $link) = $self->datasetsTable($dataset);
my $totalGeneNum = $geneNum4dataset{$dataset} || $totalGene;
my $geneNumShown;
if ($geneNum < $totalGeneNum) {
$geneNumShown = Tr(td({-colspan=>12,
-align=>'center'},
b("$geneNum of $totalGeneNum genes are displayed")));
}
return Tr(td({-colspan=>12},
hr({-size=>1,
-width=>'100%'}))).
$geneNumShown.
Tr(th({-bgcolor=>'#a4abc2',
-align=>'left',
-valign=>'top',
-rowspan=>$rowspan},
b($datasetTitle).br.$link.
br.br.
table(Tr($graph.$pearson)).
table(Tr($golink)).
$downloadLink).
th({-bgcolor=>'#b7d8e4',
-rowspan=>'2'}, "ORF").
th({-bgcolor=>'#b7d8e4',
-rowspan=>'2'}, "Gene").
th({-bgcolor=>'#b7d8e4',
-colspan=>'3'}, "Change in dataset").
th({-bgcolor=>'#b7d8e4',
-rowspan=>'2'},
"Thumbnail Display ".br.
a({-href=>url."?dataset=$dataset&id=$id&type=enlarge&expts=$expts",
-target=>'infowin'},
"(Enlarge)")).
th({-bgcolor=>'#b7d8e4',
-rowspan=>'2'}, "Similarly".br."expressed genes").
# th({-bgcolor=>'#b7d8e4',
# -rowspan=>'2'}, "Browse".br."Clustered".br."Data")).
th({-bgcolor=>'#b7d8e4',
-colspan=>'2'}, "Regulation Module")).
Tr(td({-bgcolor=>"#b7d8e4"},
"Max ".img({-border=>0,
-src=>$configUrl->dictyBaseImages."up.gif"})).
td({-bgcolor=>"#b7d8e4"},
"Max ".img({-border=>0,
-src=>$configUrl->dictyBaseImages."down.gif"})).
td({-bgcolor=>"#b7d8e4"},
"vs. other".br."datasets").
td({-bgcolor=>"#b7d8e4"},
"Regulator of").
td({-bgcolor=>"#b7d8e4"},
"Regulated by")).$rows;
}
########################################################################
sub printResultForOrf {
########################################################################
my ($self, $featNm) = @_;
if (!$featNm) {
return;
}
if (!$featNo4featNm{"\U$featNm"}) {
print "$featNm is not found in database.",p;
return;
}
my $arrayRef = Dataset->GetDatasetMaxExprChangeArrayRefBYfeatureNo(
dbh=>$dbh,
feature_no=>$featNo4featNm{"\U$featNm"});
my @dataset;
my %maxFoldUp4dataset;
my %maxFoldDown4dataset;
foreach my $rowRef (@$arrayRef) {
my ($dataset, $maxExprVal, $minExprVal) = @$rowRef;
my $maxFoldUp = $self->exprFold($maxExprVal);
my $maxFoldDown = $self->exprFold($minExprVal);
if ($exprtype =~ /^Increased$/i &&
$maxFoldUp < $fold) {
next;
}
elsif ($exprtype =~ /^Decreased$/i &&
$maxFoldDown*(-1) < $fold) {
next;
}
elsif ($exprtype =~ /^Increased or Decreased$/i &&
$maxFoldUp < $fold && $maxFoldDown*(-1) < $fold) {
next;
}
elsif ($exprtype =~ /^Not changed/i &&
($maxFoldUp >= 2 || $maxFoldDown <= -2)) {
next;
}
push(@dataset, $dataset);
$maxFoldUp4dataset{$dataset} = $maxFoldUp;
$maxFoldDown4dataset{$dataset} = $maxFoldDown;
}
if ($exprtype =~ /No Data/i) {
undef @dataset;
foreach my $dataset (keys %datasetTitle) {
if (!$maxFoldUp4dataset{$dataset} &&
!$maxFoldDown4dataset{$dataset}) {
push(@dataset, $dataset);
}
}
}
print hr({-size=>1,
-width=>'100%'});
my $showNm;
if ($gene4featNm{"\U$featNm"}) {
$showNm = $gene4featNm{"\U$featNm"}."/";
}
$showNm .= $featNm;
if (!@dataset) {
print b("No dataset found for $showNm for expression : "),
b($self->getExpressionChange), p;
return;
}
$showNm =~ s/\//\/
/;
# print h2("Results for $showNm"),p;
my $rows;
my $rowspan = 2*scalar(@dataset) + 1;
######## sort dataset #####################################
if ($sortBy =~ /Greatest to least Max Increase/i) {
undef @dataset;
foreach my $dataset (sort ({$maxFoldUp4dataset{$b} <=> $maxFoldUp4dataset{$a}} keys %maxFoldUp4dataset)) {
push(@dataset, $dataset);
}
}
elsif ($sortBy =~ /least to greatest Max Increase/i) {
undef @dataset;
foreach my $dataset (sort ({$maxFoldUp4dataset{$a} <=> $maxFoldUp4dataset{$b}} keys %maxFoldUp4dataset)) {
push(@dataset, $dataset);
}
}
elsif ($sortBy =~ /Greatest to least Max Decrease/i) {
undef @dataset;
foreach my $dataset (sort ({$maxFoldDown4dataset{$a} <=> $maxFoldDown4dataset{$b}} keys %maxFoldDown4dataset)) {
push(@dataset, $dataset);
}
}
elsif ($sortBy =~ /least to greatest Max Decrease/i) {
undef @dataset;
foreach my $dataset (sort ({$maxFoldDown4dataset{$b} <=> $maxFoldDown4dataset{$a}} keys %maxFoldDown4dataset)) {
push(@dataset, $dataset);
}
}
my $bgcolor = 'white';
foreach my $dataset (@dataset) {
my ($datasetTitle, $link) = $self->datasetsTable($dataset);
if (!$genes4dataset{$dataset} ||
!$expts4dataset{$dataset}) {
($genes4dataset{$dataset}, $expts4dataset{$dataset})
= $self->createColorStrips($dataset);
}
my $genes = $genes4dataset{$dataset};
my $expts = $expts4dataset{$dataset};
my $datasetObj = Dataset->new(dbh=>$dbh,
dataset_name=>$dataset);
my $graph = td(br);
if ($datasetObj->hasECpoint) {
$graph = td({-align=>'center'},
a({-href=>url."?orf=$featNm&dataset=$dataset&type=graph",
-target=>'infowin'},
img({-size=>10,
-border=>0,
-alt=>'GIF',
-src=>$configUrl->dictyBaseImages."cy_ball.gif"})));
}
my $regulatorUrl = $self->getRegulatorModuleUrl($dataset,
$datasetObj->dataset_no,
$featNm,
$featNo4featNm{$featNm});
my $regulator;
if ($regulatorUrl) {
$regulator = a({-href=>$regulatorUrl,
-target=>'infowin'},
img({-border=>'0',
-width=>'30',
-height=>'20',
-alt=>'regulator',
-src=>$configUrl->dictyBaseImages."reg.PNG"}));
}
else { $regulator = br; }
my @similarGenes = $self->getSimilarGenes($dataset, $featNm);
my $similar;
if (@similarGenes) {
$similar = a({-href=>url."?orf=$featNm&dataset=$dataset&type=similar",
-target=>'infowin'},
img({-border=>'0',
-size=>'10',
-alt=>'similar genes',
-src=>$configUrl->dictyBaseImages."rd_ball.PNG"}));
}
else { $similar = br; }
$rows .= Tr(td({-colspan=>9})).
Tr({-bgcolor=>$bgcolor},
td(b($datasetTitle).br.$link).
td({-align=>'center'},
$maxFoldUp4dataset{$dataset}).
td({-align=>'center'},
$maxFoldDown4dataset{$dataset}).
td({-align=>'center'},
a({-href=>url."?dataset=$dataset&orf=$featNm&type=enlarge&expts=$expts",
-target=>'infowin'},
img({-border=>'0',
-width=>'55',
-height=>'8',
-alt=>'GIF',
-src=>$configUrl->dictyBaseHtmlTmp.$featNm.".".$dataset.".gif"}))).
td({-align=>'center'},
$similar).
$graph.
td({-align=>'center'}, $regulator));
# td({-align=>'center'},
# a({-href=>$configUrl->dictyBaseCGIRoot."dictyBase/geneXplorer/geneXplorer.pl?dataset=$dataset&genes=$genes&expts=$expts",
# -target=>'infowin'},
# img({-border=>'0',
# -size=>'10',
# -alt=>'clustered',
# -src=>$configUrl->dictyBaseImages."bl_ball.gif"}))));
# td({-align=>'center'},
# a({-href=>url."?orf=$featNm&type=histogram",
# -target=>'infowin'},
# img({-border=>'0',
# -size=>'10',
# -alt=>'Histogram',
# -src=>$configUrl->dictyBaseImages."cy_ball.gif"}))).
# td($regulator));
if ($bgcolor eq "white") {
$bgcolor = "#d8d8d8";
}
else {
$bgcolor = "white";
}
}
print table({-border=>0,
-cellpadding=>1,
-cellspacing=>1},
Tr(th({-bgcolor=>'#a4abc2',
-rowspan=>$rowspan,
-valign=>'top'},
$showNm.br.br.br.
a({-href=>url."?orf=$featNm&type=histogram",
-target=>'infowin'},
"Histogram")).
th({-bgcolor=>'#b7d8e4'},
"Dataset").
th({-bgcolor=>'#b7d8e4'},
"Max Fold Increase").
th({-bgcolor=>'#b7d8e4'},
"Max Fold Decrease").
th({-bgcolor=>'#b7d8e4'},
"Display").
th({-bgcolor=>'#b7d8e4'},
"See more genes with similar expression").
th({-bgcolor=>'#b7d8e4'},
"Expression Graph").
th({-bgcolor=>'#b7d8e4'},
"Regulator of")).
$rows);
# th({-bgcolor=>'#b7d8e4'},
# "Browse Clustered Data")).$rows);
# th({-bgcolor=>'#b7d8e4'},
# "Histogram").
# th({-bgcolor=>'#b7d8e4'},
# "Regulator of")).
# $rows);
}
########################################################################
sub createDownLoadLink {
########################################################################
my ($self, $dataset, $goTerms4orfHashRef) = @_;
my $tmpfile = "$dataset.$$.tmp";
my $downloadUrl = $configUrl->dictyBaseHtmlTmp.$tmpfile;
my $tmpDir = $configPath->tmpDir;
if (-e $tmpDir.$tmpfile && param('orfs')) {
return a({-href=>$downloadUrl,
-target=>'infowin'},
"Download Data");
}
my $dataDir = $configPath->dataDir4web."dictyBase/";
my $stem = $dataDir.$dataset."/".$dataset;
my $datafile = $stem.".data";
open(IN, "$datafile") ||
die "Can't open '$datafile' for reading: $!";
my %exprData4orf;
my ($count, $exptNms);
while (){
chomp;
$count++;
my ($orf, $exprValues);
if ($_ =~ /^([^\t]+)\t(.+)$/) {
$orf = $1;
$exprValues = $2;
if ($count == 1) {
$exptNms = $exprValues;
}
elsif ($$goTerms4orfHashRef{"\U$orf"}) {
$exprData4orf{"\U$orf"} = $exprValues;
}
}
}
close(IN);
open(OUT, ">".$tmpDir.$tmpfile) ||
die "Can't open '${tmpDir}$tmpfile' for writing:$!";
print OUT "ORF\tGENE\tGO_process\tGO_function\tGO_component\t$exptNms\n";
foreach my $orf (@orf) {
my $gene = $gene4featNm{"\U$orf"};
my $goTerms = $$goTerms4orfHashRef{"\U$orf"};
my $exprValues = $exprData4orf{"\U$orf"};
print OUT "$orf\t$gene\t$goTerms\t$exprValues\n";
}
close(OUT);
return a({-href=>$downloadUrl,
-target=>'infowin'},
"Download Data");
}
########################################################################
sub createColorStrips {
########################################################################
my ($self, $dataset) = @_;
my $dataDir = $configPath->dataDir4web."dictyBase/";
my $tmpDir = $configPath->tmpDir;
my $stem = $dataDir.$dataset."/".$dataset;
my $datafile = $stem.".data";
my $giffile = $stem.".cdt.gif";
###### identify the position of the color strip in the gif file
###### for each orf.
open(IN, "$datafile") ||
die "Can't open '$datafile' for reading: $!";
my %position4featNm;
my ($expts, $genes);
while (){
chomp;
my @line = split("\t", $_, -1);
my $featNm = shift(@line);
if (!$expts) {
$expts = @line;
}
$genes++;
if (!$featNo4featNm{$featNm}) { next; }
$position4featNm{$featNm}=$.-1; # record line (-2)
}
close(IN);
$genes--;
###### create color strips
open(GIF, "$giffile") ||
die "Can't open '$giffile' for reading:$!";
my $im = new GD::Image($expts,$genes);
$im = newFromGif GD::Image(\*GIF) || die "can't make new image : $!";
close(GIF);
my $newIm = new GD::Image($expts,1);
foreach (keys %featNo4featNm){
$newIm->copy($im, 0, 0, 0, $position4featNm{$_}, $expts, 1);
open(OUT, ">$tmpDir$_.$dataset.gif")||
die "Can't make $tmpDir$_.$dataset.gif: $!";
binmode OUT;
print OUT $newIm->gif;
close OUT;
}
return ($genes, $expts);
}
########################################################################
sub showGeneList {
########################################################################
my ($self) = @_;
my $tmpfile = $configPath->tmpDir."more.".param('id');
open(IN, $tmpfile) || die "Can't open '$tmpfile' for reading:$!";
my @loci;
while() {
chomp;
@loci = split(/\:/, $_);
last;
}
close(IN);
my $loci;
foreach my $locus (@loci) {
$locus = "\U$locus";
$loci .= li(a({-href=>$locusUrl.$locus}, $locus));
}
print ul($loci), p;
}
########################################################################
sub showStatisticForDataset {
########################################################################
my ($self) = @_;
# my $totalSpot = 6200; ### it should come from database...
if (!param('dataset')) {
print "You have to pass a dataset name for displaying the statistics.", p;
return;
}
my $dataset = param('dataset');
&DeleteUnwantedChar(\$dataset);
############################################################
my $datasetObj = Dataset->new(dbh=>$dbh,
dataset_name=>$dataset);
my $totalSpot = $datasetObj->getFeatureNum;
############################################################
my $totalSpotWithDataArrayRef = Dataset->GetSpotNumArrayRef(dbh=>$dbh,
dataset_name=>$dataset);
my %totalSpotWithData4expt;
foreach my $rowRef (@$totalSpotWithDataArrayRef) {
my ($expt, $count) = @$rowRef;
$totalSpotWithData4expt{$expt} = $count;
}
### 2-fold change => log($fold)/log(2) => 1
my $fold = 2;
my $exprVal = log($fold)/log(2);
my $increasedSpotArrayRef = Dataset->GetSpotNumArrayRef(dbh=>$dbh,
dataset_name=>$dataset,
sample_value_cutoff=>$exprVal,
type=>'increased');
my %increasedSpot4expt;
foreach my $rowRef (@$increasedSpotArrayRef) {
my ($expt, $count) = @$rowRef;
$increasedSpot4expt{$expt} = $count;
}
my $decreasedSpotArrayRef = Dataset->GetSpotNumArrayRef(dbh=>$dbh,
dataset_name=>$dataset,
sample_value_cutoff=>$exprVal,
type=>'decreased');
my %decreasedSpot4expt;
foreach my $rowRef (@$decreasedSpotArrayRef) {
my ($expt, $count) = @$rowRef;
$decreasedSpot4expt{$expt} = $count;
}
my $sampleArrayRef = Dataset->GetSamplesArrayRef(dbh=>$dbh,
dataset_name=>$dataset);
########
########
my $linkUrl = url."?dataset=$dataset&fold=2&option=option3&exprtype=";
my $rows;
foreach my $rowRef (@$sampleArrayRef) {
my ($expt, $unit) = @$rowRef;
my $increased =
$self->percentCal($increasedSpot4expt{$expt}*100/$totalSpot);
my $decreased =
$self->percentCal($decreasedSpot4expt{$expt}*100/$totalSpot);
my $changed = $increased + $decreased;
my $notChanged =
$self->percentCal($totalSpotWithData4expt{$expt}*100/$totalSpot
- $changed);
my $noData = $self->percentCal(100 - $notChanged - $changed);
$rows .= Tr(td({-bgcolor=>'#b7d8e4'},
$expt." ".$unit).
td({-align=>'center'},
a({-href=>$linkUrl."Increased",
-target=>'infowin'},
$increased.'%')).
td({-align=>'center'},
a({-href=>$linkUrl."Decreased",
-target=>'infowin'},
$decreased.'%')).
td({-align=>'center'},
a({-href=>$linkUrl."Increased+or+Decreased",
-target=>'infowin'},
$changed.'%')).
td({-align=>'center'},
a({-href=>$linkUrl."Not+changed",
-target=>'infowin'},
$notChanged.'%')).
td({-align=>'center'},
a({-href=>$linkUrl."No+Data",
-target=>'infowin'},
$noData.'%')).
td({-align=>'center'}, $totalSpot));
}
my $datasetTitle = $datasetObj->title;
print center(font({-size=>'+2'}, b("Global Statistics for Dataset: $datasetTitle"))),p;
print table({-align=>'center',
-border=>1,
-cellpadding=>2},
Tr({-bgcolor=>'#a4abc2'},
td({-colspan=>'7'},
font({-size=>'+2'},
b("Percent of Spots Changing, By Experiment")))).
Tr(th({-rowspan=>2},
"Experiment").
th({-colspan=>6},
"Expression")).
Tr({-bgcolor=>'#b7d8e4',
-align=>'center'},
th("Increased").
th("Decreased").
th("Increased".br."or".br."Decreased").
th("No Change").
th("Not Expressed/".br."No Data").
th("Number of".br."spots in".br."experiments")).
$rows),p;
print center("* Increased or Decreased relative to control by $fold-fold or greater."),p;
}
########################################################################
sub percentCal {
########################################################################
my ($self, $percent) = @_;
if ($percent =~ /^([0-9]+\.[0-9])([0-9])/) {
$percent = $1;
if ($2 >= 5) { $percent += 0.1; }
}
if ($percent < 0.001) { $percent = 0; }
return $percent;
}
########################################################################
sub printSearchParamForOption1 {
########################################################################
my ($self) = @_;
my $locusList = $self->getGeneList;
my $datasetList = $self->getDatasetList;
print table({-width=>'100%'},
Tr(td(b("Search: ")."Find how a single gene's or multiple gene's expression changes in one or more datasets")).
Tr(td(b("Gene Name(s): ").$locusList)).
Tr(td(b("Datasets selected").ul($datasetList))));
}
########################################################################
sub printSearchParamForOption2 {
########################################################################
my ($self) = @_;
my $locusList = $self->getGeneList;
my $expressionChange = $self->getExpressionChange;
print table({-width=>'100%'},
Tr(td(b("Search: ")."Find datasets where the expression of one or more genes changes by an amount you define.")).
Tr(td(b("Gene Name(s): ").$locusList)).
Tr(td(b("Expression change: ").$expressionChange)));
}
########################################################################
sub printSearchParamForOption3 {
########################################################################
my ($self) = @_;
my $datasetList = $self->getDatasetList;
my $expressionChange = $self->getExpressionChange;
print table({-width=>'100%'},
Tr(td(b("Search: ")."Find genes where the expression changes in one or more datasets by an amount you define.")).
Tr(td(b("Expression change: ").$expressionChange)).
Tr(td(b("Datasets selected").ul($datasetList))));
}
########################################################################
sub getExpressionChange {
########################################################################
my ($self) = @_;
my $fold = param('fold') || "2 (by default)";
if (param('exprtype') =~ /^(Increased|Decreased)/i) {
return param('exprtype')." ".b("by")." ".$fold." ".b("fold");
}
else {
return param('exprtype');
}
}
########################################################################
sub getGeneList {
########################################################################
my ($self) = @_;
$loci =~ s/[\t\n\r]+/ /g;
$loci =~ s/ +/\:/g;
my @loci = split(/:/, $loci);
my $locusList;
my $count;
my $moreList;
foreach my $gene (@loci) {
my $locus = $gene4featNm{$gene} || $gene;
$count++;
if ($count <= 10) {
$locus = "\U$locus";
if ($locusList) {
$locusList .= ", ";
}
$locusList .= a({-href=>$locusUrl.$gene}, $locus);
}
if ($moreList) { $moreList .= ":"; }
$moreList .= $locus;
}
if ($count > 10) {
$locusList .= ", ".a({-href=>url."?more=1&id=$$",
-target=>'infowin'},
"More");
}
open(OUT, ">".$configPath->tmpDir."more.$$") ||
die "Can't open '".$configPath->tmpDir."more.$$' for writing:$!";
print OUT $moreList, "\n";
close(OUT);
return $locusList;
}
########################################################################
sub getDatasetList {
########################################################################
my ($self) = @_;
my $datasetList;
foreach my $dataset (@dataset) {
my $geneNum;
if (param('submit3') || param('option') =~ /option3/i) {
$geneNum = $geneNum4dataset{$dataset};
}
else {
$geneNum = $totalGene;
}
if ($geneNum > 1) { $geneNum .= " genes"; }
else { $geneNum .= " gene"; }
$geneNum = " ($geneNum)";
$datasetList .= li(a({-href=>"#$dataset"},
$datasetTitle{$dataset}).$geneNum);
}
return $datasetList;
}
########################################################################
sub getRegulatorModuleUrl {
########################################################################
my ($self, $dataset, $datasetNo, $featNm, $featNo) = @_;
my $regulatorModuleArrayRef =
Dataset->RegulatorModuleArrayRef(dbh=>$dbh,
dataset_no=>$datasetNo,
feature_no=>$featNo);
if (!@$regulatorModuleArrayRef) { return ; }
if (@$regulatorModuleArrayRef == 1) {
my $rowRef = $$regulatorModuleArrayRef[0];
my ($module) = @$rowRef;
$module =~ s/^Module ([0-9]+)$/cluster_${1}\.html/i;
return $configUrl->wineServerRoot."Dictyostelium/exp_modules/$dataset/$module";
}
return url."?dataset=$dataset&orf=$featNm&type=regulator";
}
########################################################################
sub printDescription {
########################################################################
my ($self) = @_;
my $cubeImage = $configUrl->dictyBaseImages."redcube.PNG";
print "";
print table({-align=>'center',
-border=>'0',
-cellpadding=>'0',
-cellspacing=>'0',
-width=>'100%'},
Tr(td({-align=>'center'},
h2("Expression Connection allows you to search gene expression data from multiple microarray studies."))).
Tr(td(table({-align=>'center',
-width=>'80%'},
Tr(td({-align=>'left'},
blockquote(b(a({-href=>'#Option1'},
img({-width=>'10',
-alt=>'bullet',
-src=>$cubeImage})).
" ".a({-href=>'#Option1'}, "Search I").": Find the expression of one or more genes in one or more datasets. ".
br.br.
a({-href=>'#Option2'},
img({-width=>'10',
-alt=>'bullet',
-src=>$cubeImage})).
" ".a({-href=>'#Option2'}, "Search II").": Find datasets where the expression of one or more genes changes by an amount you define. ".
br.br.
a({-href=>'#Option3'},
img({-width=>'10',
-alt=>'bullet',
-src=>$cubeImage})).
" ".a({-href=>'#Option3'}, "Search III").": Find all genes that change expression in a manner you define in one or more datasets (eg. increase by 10-fold). ".
br.br.
a({-href=>$configUrl->breadServerRoot."webminer/"},
img({-width=>'10',
-alt=>'bullet',
-src=>$cubeImage})).
" ".a({-href=>$configUrl->breadServerRoot."webminer/"}, "Webminer").": Search microarray datasets on an experiment by experiment basis ".
br.br.
a({-href=>'#Additional'},
img({-width=>'10',
-alt=>'bullet',
-src=>$cubeImage})).
" ".a({-href=>$configUrl->dictyBaseHelp.'Expression.html#other'}, "Other Resources").": Go to websites outside of dictyBase. ")))))))),p;
}
########################################################################
sub printOption1 {
########################################################################
my ($self) = @_;
my $subtitle = " Search I: Find the expression of one or more genes in one or more datasets.";
print start_multipart_form;
print hidden(-name=>'option',
-value=>'option1');
print "";
print table({-border=>'0',
-cellpadding=>'10',
-cellspacing=>'0',
-width=>'100%'},
$self->subtitleRow($subtitle).
Tr(td({-colspan=>'3'},
blockquote($self->option1)))
);
print end_form;
}
########################################################################
sub printOption2 {
########################################################################
my ($self) = @_;
my $subtitle = " Search II: Find datasets where the expression of one or more genes changes by an amount you define.";
print "";
print start_multipart_form;
print hidden(-name=>'option',
-value=>'option2');
print table({-border=>'0',
-cellpadding=>'10',
-cellspacing=>'0',
-width=>'100%'},
$self->subtitleRow($subtitle).
Tr(td({-colspan=>'3'},
blockquote($self->option2)))
);
print end_form;
}
########################################################################
sub printOption3 {
########################################################################
my ($self) = @_;
my $subtitle = " Search III: Find all genes that change expression in a manner you define in one or more datasets (eg. increase by 10-fold).";
print "";
print start_form;
print hidden(-name=>'option',
-value=>'option3');
print table({-border=>'0',
-cellpadding=>'10',
-cellspacing=>'0',
-width=>'100%'},
$self->subtitleRow($subtitle).
Tr(td({-colspan=>'3'},
blockquote($self->option3)))
);
print end_form;
}
########################################################################
sub option1 {
########################################################################
my ($self) = @_;
my @orf = param('ORFs');
my $loci = join(' ', @orf);
return table({-border=>'1',
-cellpadding=>'10',
-width=>'100%'},
$self->stepRow("Step 1. Specify gene name(s):").
Tr(td(table({-border=>'0'},
Tr(td({-width=>'40%',
-valign=>'top'},
b("Enter gene name(s) separated by \"Return\":").br.
textarea(-name=>'loci',
-value=>$loci,
-cols=>'10',
-rows=>'10')).
td({-valign=>'top'},
font({-color=>'red',
-size=>'+2'},
b("OR"))).
td({-width=>'40%',
-valign=>'top'},
b("Select TEXT file with list of ORF or gene names, one per line. WORD Documents do not work unless saved as TEXT:").br.
filefield(-name=>'uploadfile')))))).
$self->stepRow("Step 2. Select datasets you wish to query:").
Tr(td(table({-border=>'0'},
Tr(td($self->datasetsTable))))).
$self->stepRow("Step 3. ".
submit(-name=>'submit1',
-value=>'Submit').' '.
reset(-name=>'Reset'))
);
}
########################################################################
sub option2 {
########################################################################
my ($self) = @_;
my @orf = param('ORFs');
my $loci = join(' ', @orf);
return table({-border=>'1',
-cellpadding=>'10',
-width=>'100%'},
$self->stepRow("Step 1. Specify gene name(s):").
Tr(td(table({-border=>'0'},
Tr(td({-width=>'40%',
-valign=>'top'},
b("Enter gene name(s) separated by \"Return\":").br.
textarea(-name=>'loci',
-value=>$loci,
-cols=>'10',
-rows=>'10')).
td({-valign=>'top'},
font({-color=>'red',
-size=>'+2'},
b("OR"))).
td({-width=>'40%',
-valign=>'top'},
b("Select TEXT file with list of ORF or gene names, one per line. WORD Documents do not work unless saved as TEXT:").br.
filefield(-name=>'uploadfile')))))).
$self->stepRow("Step 2. Choose expression change:").
Tr(td(table({-border=>'0'},
Tr(td(b("Get experiments where gene expression is").br.
$self->popup))))).
$self->stepRow("Step 3. ".
submit(-name=>'submit2',
-value=>'Submit').' '.
reset(-name=>'Reset'))
);
}
########################################################################
sub option3 {
########################################################################
my ($self) = @_;
return table({-border=>'1',
-cellpadding=>'10',
-width=>'100%'},
$self->stepRow("Step 1. Choose expression change:").
Tr(td(table({-border=>'0'},
Tr(td(b("Get all genes that are ").br.
$self->popup))))).
$self->stepRow("Step 2. Select datasets you wish to query:").
Tr(td(table({-border=>'0'},
Tr(td($self->datasetsTable))))).
$self->stepRow("Step 3. ".
submit(-name=>'submit3',
-value=>'Submit').' '.
reset(-name=>'Reset'))
);
}
########################################################################
sub datasetsTable {
########################################################################
my ($self, $dataset) = @_;
my $refUrl = $configUrl->dictyBaseCGIRoot."$dblink/reference/reference.pl?refNo=";
my $statisticUrl = url."?type=statistic&dataset=";
my $datasetArrayRef = Dataset->GetDatasetInfoArrayRef(dbh=>$dbh);
my ($rows, $preDatasetNm, $datasetSrc, $datasetTitle,
$authors, $link, $reflist);
foreach my $rowRef (@$datasetArrayRef) {
my ($datasetNo, $datasetNm, $source, $title, $refNo,
$citation) = @$rowRef;
if ($dataset && "\U$datasetNm" ne "\U$dataset") { next; }
$citation =~ s/^(.+)\([0-9]{4}\) [A-Z].+$/$1/;
$citation = b($citation).
a({-href=>$refUrl.$refNo,
-target=>'infowin'},
img({-src=>$configUrl->dictyBaseImages."dictyBaserefsml.gif",
-border=>0}));
if ($datasetNm eq $preDatasetNm) {
#$authors .= " | ".$citation;
$reflist .= br.$citation." ".$link;
next;
}
if ($datasetTitle) {
# $rows .= Tr(td(checkbox(-name=>'dataset',
# -value=>$preDatasetNm,
# -label=>'')." ".
# b($datasetTitle).", ".$datasetSrc).
# td($authors." | ".$link));
$rows .= Tr(td(checkbox(-name=>'dataset',
-value=>$preDatasetNm,
-label=>'')." ".
b($datasetTitle).", ".$datasetSrc).
td($reflist));
}
$datasetTitle = $title;
$datasetSrc = $source;
# $authors = $citation;
my $datasetObj = Dataset->new(dbh=>$dbh,
dataset_no=>$datasetNo);
my $website = br;
if ($datasetObj) {
$website = a({-href=>$datasetObj->web_site_url,
-target=>'infowin'},
img({-src=>$configUrl->dictyBaseImages."webSupplement.gif",
-border=>0}));
}
my $statistics = a({-href=>$statisticUrl.$datasetNm,
-target=>'infowin'},
img({-src=>$configUrl->dictyBaseImages."statsg2.PNG",
-width=>45,
-border=>0}));
$link = $website." ".$statistics;
if ($datasetObj->isInDatasetGroup) {
$link .= " ".a({-href=>$configUrl->wineServerRoot."Dictyostelium/exp_modules/$dataset/index.html",
-target=>'infowin'},
img({-src=>$configUrl->dictyBaseImages."reg.PNG",
-width=>32,
-border=>0}));
}
if ($citation =~ /Spellman/i) {
$link .= br.font({-size=>'-1'}, "The analysis in Spellman et al included data from ".a({-href=>$refUrl.'19633'}, "Cho et al"));
}
$reflist = $citation." ".$link;
$preDatasetNm = $datasetNm;
}
if ($dataset) {
# return ($datasetTitle, $authors." | ".$link);
return ($datasetTitle, $reflist);
}
$rows .= Tr(td(checkbox(-name=>'dataset',
-value=>$preDatasetNm,
-label=>'')." ".
b($datasetTitle).", ".$datasetSrc).
td($reflist));
return table({-bgcolor=>'#FFFFFF',
-border=>'2',
-cellpadding=>'5',
-cellspacing=>'0',
-width=>'100%'},
$rows);
}
########################################################################
sub golinks {
########################################################################
my ($self, $orfArrayRef, $dataset, $downloadLink) = @_;
my $formName1 = "goTermMapperForm_".$dataset;
my $formName2 = "goTermFinderForm_".$dataset;
my $formName3 = "goSummary_".$dataset;
return start_form(-action=>$configUrl->dictyBaseCGIRoot."$dblink/GO/goTermMapper",
-name=>$formName1,
-target=>"infowin").
hidden(-name=>'ORFs',
-value=>$orfArrayRef).
a({-href=>"javascript:document.$formName1.submit()"},
"GO Term Mapper").end_form.br.
start_form(-action=>$configUrl->dictyBaseCGIRoot."$dblink/GO/goTermFinder",
-name=>$formName2,
-target=>"infowin").
hidden(-name=>'ORFs',
-value=>$orfArrayRef).
a({-href=>"javascript:document.$formName2.submit()"},
"GO Term Finder").end_form.br.
start_form(-action=>$configUrl->dictyBaseCGIRoot."$dblink/GO/GOreport.pl",
-name=>$formName3,
-target=>"infowin").
hidden(-name=>'similarORFs',
-value=>$orfArrayRef).
a({-href=>"javascript:document.$formName3.submit()"},
"View GO Annotation Summary").end_form.br.
$downloadLink;
}
########################################################################
sub manageGeneList {
########################################################################
my ($self, $orfArrayRef, $dataset, $goTerm4orfHashRef) = @_;
my $download = $self->createDownLoadLink($dataset, $goTerm4orfHashRef);
my $formName1 = "goTermMapperForm_".$dataset.$$;
my $formName2 = "goTermFinderForm_".$dataset.$$;
my $formName3 = "goSummaryForm_".$dataset.$$;
print p, table({-align=>'center',
-border=>'2',
-width=>'100%'},
Tr(th({-bgcolor=>'#b7d8e4'},
"Analyze gene list with:").
td({-align=>'center'},
br.start_form(-action=>$configUrl->dictyBaseCGIRoot."$dblink/GO/goTermFinder",
-name=>$formName1,
-target=>"infowin").
hidden(-name=>'ORFs',
-value=>$orfArrayRef).
a({-href=>"javascript:document.$formName1.submit()"},
"GO Term Finder").end_form).
td({-align=>'center'},
br.start_form(-action=>$configUrl->dictyBaseCGIRoot."$dblink/GO/goTermMapper",
-name=>$formName2,
-target=>"infowin").
hidden(-name=>'ORFs',
-value=>$orfArrayRef).
a({-href=>"javascript:document.$formName2.submit()"},
"GO Term Mapper").end_form)).
Tr(th({-bgcolor=>'#b7d8e4'},
"Manage gene list with:").
td({-align=>'center'},
br.start_form(-action=>$configUrl->dictyBaseCGIRoot."$dblink/GO/GOreport.pl",
-name=>$formName3,
-target=>"infowin").
hidden(-name=>'similarORFs',
-value=>$orfArrayRef).
a({-href=>"javascript:document.$formName3.submit()"},
"View GO Annotation Summary").end_form).
td({-align=>'center'},
$download)));
}
########################################################################
sub popup {
########################################################################
my ($self) = @_;
return popup_menu(-name=>'exprtype',
-value=>['-Select-',
'Increased',
'Decreased',
'Increased or Decreased',
'Not Changed',
'Not Expression/No Data']).
b(" by ").
textfield(-name=>'fold',
-size=>'10').
b(" fold. (Enter a positive integer greater than or equal to 2)");
}
########################################################################
sub stepRow {
########################################################################
my ($self, $stepTitle) = @_;
return Tr(td({-bgcolor=>'#b7d8e4',
-colspan=>'3'},
font({-size=>'+1'},
$stepTitle)));
}
########################################################################
sub subtitleRow {
########################################################################
my ($self, $subtitle) = @_;
return Tr({-width=>'100%',
-bgcolor=>'#a4abc2'},
td(font({-size=>'+2'},
a({-href=>'#top'},
img({-width=>'17',
-alt=>'bullet',
-src=>$cubeImage})).
$subtitle)).
td(a({-href=>'#top'},
"Back to top")));
}
########################################################################
sub printSubtitle {
########################################################################
my ($self, $subtitle) = @_;
print table({-width=>'100%'},
Tr({-bgcolor=>'#a4abc2'},
td({-align=>'left'},
h2($subtitle))));
}
########################################################################
sub printScaleEtc1 {
########################################################################
my ($self) = @_;
##### force it to overwrite the value for loci parameter
param('loci', $loci);
print table(Tr(td(b("Scale"))).
Tr(td(img({-border=>0,
-valign=>'bottom',
-width=>350,
-src=>$configUrl->dictyBaseImages."scale.1.5.gif"})." ").
td({-valign=>'bottom'},
start_form.
popup_menu(-name=>'sortBy',
-values=>['- Sort genes in datasets -',
'Alphabetically, by ORF name',
'Greatest to least Max Increase',
'Least to greatest Max Increase',
'Greatest to least Max Decrease',
'Least to greatest Max Decrease'],
-default=>param('sortBy')).
hidden(-name=>'dataset',
-value=>\@dataset).
hidden(-name=>'loci',
-value=>$loci).
hidden(-name=>'option',
-value=>'option1').
hidden(-name=>'showGeneNum',
-value=>param('showGeneNum')).
submit(-name=>'sortSubmit',
-value=>'Go').
end_form).
td({-valign=>'bottom',
-align=>'right'},
start_form.
# submit(-name=>'downloadSubmit',
# -value=>'Download Data').
submit(-name=>'newSearchSubmit',
-value=>'New Search').
end_form)));
}
########################################################################
sub printScaleEtc2 {
########################################################################
my ($self) = @_;
print table(Tr(td(b("Scale"))).
Tr(td(img({-border=>0,
-valign=>'bottom',
-width=>350,
-src=>$configUrl->dictyBaseImages."scale.1.5.gif"})." ").
td({-valign=>'bottom'},
start_form.
popup_menu(-name=>'sortBy',
-values=>['- Sort datasets -',
'Greatest to least Max Increase',
'Least to greatest Max Increase',
'Greatest to least Max Decrease',
'Least to greatest Max Decrease'],
-default=>param('sortBy')).
hidden(-name=>'loci',
-value=>$loci).
hidden(-name=>'exprtype',
-value=>param('exprtype')).
hidden(-name=>'fold',
-value=>param('fold')).
hidden(-name=>'option',
-value=>'option2').
submit(-name=>'sortSubmit',
-value=>'Go').
end_form).
td({-valign=>'bottom',
-align=>'right'},
start_form.
# submit(-name=>'downloadSubmit',
# -value=>'Download Data').
submit(-name=>'newSearchSubmit',
-value=>'New Search').
end_form)));
}
########################################################################
sub printScaleEtc3 {
########################################################################
my ($self) = @_;
print table(Tr(td(b("Scale"))).
Tr(td(img({-border=>0,
-valign=>'bottom',
-width=>350,
-src=>$configUrl->dictyBaseImages."scale.1.5.gif"})." ").
td({-valign=>'bottom'},
start_form.
popup_menu(-name=>'sortBy',
-values=>['- Sort genes in datasets -',
'Alphabetically, by ORF name',
'Greatest to least Max Increase',
'Least to greatest Max Increase',
'Greatest to least Max Decrease',
'Least to greatest Max Decrease'],
-default=>param('sortBy')).
hidden(-name=>'dataset',
-value=>\@dataset).
hidden(-name=>'exprtype',
-value=>param('exprtype')).
hidden(-name=>'fold',
-value=>param('fold')).
hidden(-name=>'option',
-value=>'option3').
hidden(-name=>'showGeneNum',
-value=>param('showGeneNum')).
submit(-name=>'sortSubmit',
-value=>'Go').
end_form).
td({-valign=>'bottom',
-align=>'right'},
start_form.
# submit(-name=>'downloadSubmit',
# -value=>'Download Data').
submit(-name=>'newSearchSubmit',
-value=>'New Search').
end_form)));
}
########################################################################
sub moreLink {
########################################################################
my ($self, @loci) = @_;
my $formName = "excn".$$;
return
start_form(-action=>url,
-name=>$formName,
-target=>'infowin').
hidden(-name=>'more',
-value=>1).
hidden(-name=>'gene',
-value=>\@loci).
a({-href=>"javascript:document.$formName.submit()"},
"More").
end_form;
}
########################################################################
# sub additionalSearch {
########################################################################
# my ($self) = @_;
# print "";
# print table({-width=>'100%'},
# Tr(td(b("Additional searches can be found at these sites:").
# br.
# a({-href=>'http://transcriptome.ens.fr/ymgv/'},
# "Dictyostelium Microarray Global Viewer").
# " at the Laboratories de genetique moleculaire, Paris, France").
# td(a({-href=>'#top'},
# "Back to top"))));
# }
########################################################################
sub lineSeparator {
########################################################################
print hr({-noshade=>1,
-size=>5,
-color=>'#000000'});
}
########################################################################
sub exprFold {
########################################################################
my ($self, $exprLogVal) = @_;
if (!$exprLogVal) {
return "1.0";
}
my ($sign, $exprFold);
if ($exprLogVal < 0) {
$sign = "-";
$exprLogVal =~ s/^\-//;
}
$exprFold = 2**$exprLogVal;
if ($exprFold =~ /^([0-9]+\.[0-9])([0-9])/) {
$exprFold = $1;
if ($2 >= 5) { $exprFold += 0.1; }
}
else {
$exprFold .= ".0";
}
return $sign.$exprFold;
}
########################################################################
sub setVariables {
########################################################################
my ($self) = @_;
$configUrl = ConfigURLdictyBase->new;
$dblink = $configUrl->dblink($self->database);
$configPath = ConfigPathdictyBase->new;
$cubeImage = $configUrl->dictyBaseImages."redcube.PNG";
if (!param) { return; }
if (param('showGeneNum')) {
$maxDisplayNum = param('showGeneNum');
}
$locusUrl = $configUrl->dictyBaseCGIRoot."gene_page.pl?gene_name=";
if (param('loci') && param('uploadfile')) {
$self->err_report("You can enter gene names OR select a file to upload for search option 1 or 2.");
exit;
}
if (param('loci')) {
$loci = param('loci');
$loci =~ s/[\n\r\f\t ]/\:/g;
}
elsif (param('uploadfile')) {
my $fh = upload('uploadfile');
while(<$fh>) {
chomp;
$_ =~ s/\t/ /g;
my ($locus, $others) = split(/ /);
$locus =~ s/\15/:/g;
$locus =~ s/\:+/\:/g;
&DeleteUnwantedChar(\$locus);
if (!$locus) { next; }
$loci .= ":".$locus;
}
}
elsif (param('dataset') && param('orf')) {
$loci = param('orf');
&DeleteUnwantedChar(\$loci);
}
$loci =~ s/\:+/\:/g;
$loci =~ s/^\://;
if ( (param('submit1') || param('submit2') ||
param('option') =~ /option(1|2)/i) && !$loci ) {
$self->err_report("You must enter one or more genes for search option 1 or 2.");
exit;
}
@dataset = param('dataset');
if ( (param('submit1') || param('submit3') ||
param('option') =~ /option(1|3)/i) && !@dataset ) {
$self->err_report("You have to choose one or more datasets for search option 1 or 3.");
exit;
}
$exprtype = param('exprtype');
$exprtype =~ s/^-Select-.*$//;
$fold = param('fold');
&DeleteUnwantedChar(\$fold);
# if ($fold < 2) {
# $self->err_report("You have to enter a positive integer greater than or equal to 2 for search option 2 or 3.");
# exit;
# }
if ( param('submit2') || param('submit3') ||
param('option') =~ /option(2|3)/i) {
if (!$exprtype) {
$self->err_report("You have to select the expression change pattern for search option 2 or 3.");
exit;
}
elsif ($exprtype =~ /(Increased|Decreased)/i &&
($fold !~ /^[0-9]+$/ || $fold < 2) ) {
$self->err_report("You have to enter a positive integer greater than or equal to 2 for the expression increased/decreased fold.");
exit;
}
}
$sortBy = param('sortBy');
my $datasetArrayRef = Dataset->GetDatasetInfoArrayRef(dbh=>$dbh);
foreach my $rowRef (@$datasetArrayRef) {
my ($datasetNo, $datasetNm, $source, $title, $others) = @$rowRef;
$datasetTitle{$datasetNm} = $title;
}
if (param('submit1') || param('option') =~ /^option1/i ||
param('submit3') || param('option') =~ /^option3/i) {
my $arrayRef = Feature->GetAllFeatInfoArrayRef(dbh=>$dbh);
foreach my $rowRef (@$arrayRef) {
my ($featNm, $featNo, $locus, $others) = @$rowRef;
$featNo4featNmInAll{"\U$featNm"} = $featNo;
$gene4featNmInAll{"\U$featNm"} = $locus;
$featNm4geneInAll{"\U$locus"} = $featNm;
}
}
if (!$loci) { return; }
my @loci = split(/:/, $loci);
my $count;
my @validLoci;
foreach my $query (@loci) {
my ($featNm, $featNo, $locusNm);
if ($featNm4geneInAll{"\U$query"}) {
$locusNm = "\U$query";
$featNm = $featNm4geneInAll{$locusNm};
$featNo = $featNo4featNmInAll{"\U$featNm"};
}
elsif ($gene4featNmInAll{"\U$query"}) {
$featNm = "\U$query";
$locusNm = $gene4featNmInAll{$featNm};
$featNo = $featNo4featNmInAll{$featNm};
}
else {
my $seqObj = SeqParamTranslator->new(dbh=>$dbh,
query=>$query);
if ($seqObj->error) {
if ($self->{'_notFound'}) {
$self->{'_notFound'} .= ", ";
}
$self->{'_notFound'} .= $query;
next;
}
if ($seqObj->featureObject) {
$featNm = $seqObj->featureObject->feature_name;
$featNo = $seqObj->featureObject->feature_no;
$locusNm = $seqObj->featureObject->locus_name;
}
else {
if ($self->{'_noORFassociated'}) {
$self->{'_noORFassociated'} .= ", ";
}
$self->{'_noORFassociated'} .= $query;
}
}
if ($featNm) {
$featNo4featNm{$featNm} = $featNo;
$gene4featNm{$featNm} = $locusNm;
push(@orf, $featNm);
push(@validLoci, $query);
}
}
$totalGene = scalar(@validLoci);
$loci = join(':', @validLoci);
$self->{'_noORFassociated'} =~ s/^(.+, .+,) ([^\,]+)$/$1 and $2/;
$self->{'_notFound'} =~ s/^(.+, .+,) ([^\,]+$)/$1 and $2/;
$self->{'_noORFassociated'} =~ s/^([^\,]+), ([^\,]+)$/$1 and $2/;
$self->{'_notFound'} =~ s/^([^\,]+), ([^\,]+)$/$1 and $2/;
if ($self->{'_noORFassociated'}) {
$self->{'_error'} = "No feature_name associated with gene ".$self->{'_noORFassociated'}.". ";
}
if ($self->{'_notFound'}) {
$self->{'_error'} .= p."The ".$self->{'_notFound'};
if ($self->{'_notFound'} !~ / and /) {
$self->{'_error'} .= " is not a valid gene name.";
}
else {
$self->{'_error'} .= " are not valid gene names.";
}
}
if (!$totalGene) {
$self->{'_error'} .= p."Please enter a valid gene/ORF name. See ".a({-href=>$configUrl->breadServerRoot."Dictyostelium/gene_guidelines.html"}, "Gene Naming Guidelines")." for more help.".p;
$self->err_report($self->{'_error'});
exit;
}
}
########################################################################
sub getSimilarGenes {
########################################################################
my ($self, $dataset, $featNm) = @_;
my $dataDir = $configPath->dataDir4web."dictyBase/";
my $stem = $dataDir.$dataset."/".$dataset;
my $corFile = $stem.".stdCor";
open(COR, $corFile) ||
die "Can't open '$corFile' for reading:$!";
my @similarGenes;
while() {
chomp;
next unless (/^$featNm\t/i || /^$featNm$/i);
@similarGenes = split(/\t/);
last;
}
return @similarGenes;
}
########################################################################
sub setGeneList {
########################################################################
my ($self, $dataset, $id) = @_;
undef %featNo4featNm;
undef %gene4featNm;
undef @orf;
undef $loci;
my $arrayRef = Dataset->GetGeneNameArrayRefBYdataset(dbh=>$dbh,
dataset_name=>$dataset);
$totalGene = scalar(@$arrayRef);
my $count;
foreach my $rowRef (@$arrayRef) {
my ($featNm, $maxExprVal, $minExprVal) = @$rowRef;
my $maxFoldUp = $self->exprFold($maxExprVal);
my $maxFoldDown = $self->exprFold($minExprVal);
if ($exprtype =~ /^Increased$/i &&
$maxFoldUp < $fold) {
next;
}
elsif ($exprtype =~ /^Decreased$/i &&
$maxFoldDown*(-1) < $fold) {
next;
}
elsif ($exprtype =~ /^Increased or Decreased$/i &&
$maxFoldUp < $fold && $maxFoldDown*(-1) < $fold) {
next;
}
elsif ($exprtype =~ /^Not changed/i &&
($maxFoldUp > 2 || $maxFoldDown < -2)) {
next;
}
$count++;
# if ($count > $maxDisplayNum && !param('whole')) { last; }
if ($loci) { $loci .= ":"; }
$loci .= $featNm;
push(@orf, $featNm);
$featNo4featNm{$featNm} = $featNo4featNmInAll{"\U$featNm"};
$gene4featNm{$featNm} = $gene4featNmInAll{"\U$featNm"};
}
my $tmpfile = $configPath->tmpDir."more.$id";
open(TMP, ">$tmpfile") || die "Can't open '$tmpfile' for writing:$!";
print TMP $loci;
close(TMP);
}
########################################################################
sub err_report {
########################################################################
my ($self, $err) = @_;
&printStartPage($self->database, $self->title, $self->help);
print $err;
&printEndPage;
exit;
}
########################################################################
1; #####################################################################
########################################################################