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gensel_class.php
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gensel_class.php
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<?php
namespace T3;
/**
* Using a PHP class to implement the "Download Gateway" feature
*
* @author Clay Birkett <clb343@cornell.edu>
* @license http://triticeaetoolbox.org/wheat/docs/LICENSE Berkeley-based
* @link http://triticeaetoolbox.org/wheat/downloads/downloads.php
**/
class Downloads
{
/**
* Delimiter used for output files
*/
public $delimiter = "\t";
/**
* Using the class's constructor to decide which action to perform
*
* @param string $function action to perform
*/
public function __construct($function = null)
{
switch ($function) {
case 'genomic_prediction':
$this->genomic_prediction();
break;
case 'run_histo':
$this->run_histo();
break;
case 'run_gwa':
$this->run_gwa();
break;
case 'run_gwa2':
$this->run_gwa2();
break;
case 'run_rscript':
$this->run_rscript();
break;
case 'run_rscript2':
$this->run_rscript2();
break;
case 'download_session_v2':
$this->type1_session(V2);
break;
case 'download_session_v3':
$this->type1_session(V3);
break;
case 'download_session_v4':
$this->type1_session(V4);
break;
case 'refreshtitle':
$this->refreshTitle();
break;
case 'gwas_status':
$this->status_gwas();
break;
case 'pred_status':
$this->status_pred();
break;
case 'filter_lines':
$this->filterLines();
break;
case 'web':
$this->type1Select();
break;
}
}
/**
* Load header and footer then check session to use existing data selection
*/
private function type1Select()
{
global $config;
global $mysqli;
require_once $config['root_dir'].'theme/normal_header.php';
$phenotype = "";
$lines = "";
$markers = "";
$saved_session = "";
$this->type1Checksession();
require_once 'downloads/select-map.php';
require_once $config['root_dir'].'theme/footer.php';
}
/**
* Checks the session variable, if there is lines data saved then go directly to the lines menu
*/
private function type1Checksession()
{
global $mysqli;
?>
<style type="text/css">
th {background: #5B53A6 !important; color: white !important; border-left: 2px solid #5B53A6}
table {background: none; border-collapse: collapse}
td {border: 1px solid #eee !important;}
h3 {border-left: 4px solid #5B53A6; padding-left: .5em;}
</style>
<link rel="stylesheet" href="//code.jquery.com/ui/1.12.1/themes/smoothness/jquery-ui.css">
<script type="text/javascript" src="downloads/download_gs04.js"></script>
<script type="text/javascript" src="downloads/downloadsjq03.js"></script>
<div id="title">
<?php
$phenotype = "";
$lines = "";
$markers = "";
$saved_session = "";
$message1 = $message2 = "";
if (isset($_SESSION['phenotype'])) {
$tmp = count($_SESSION['phenotype']);
if ($tmp==1) {
$saved_session = "$tmp phenotype ";
} else {
$saved_session = "$tmp phenotypes ";
}
$message2 = "download phenotype and genotype data";
$phenotype = $_SESSION['phenotype'];
} else {
$message1 = "0 phenotypes";
$message2 = " download genotype data";
}
if (isset($_SESSION['selected_lines'])) {
$countLines = count($_SESSION['selected_lines']);
if ($saved_session == "") {
$saved_session = "$countLines lines";
} else {
$saved_session = $saved_session . ", $countLines lines";
}
$lines = $_SESSION['selected_lines'];
}
if (isset($_SESSION['clicked_buttons'])) {
$tmp = count($_SESSION['clicked_buttons']);
$saved_session = $saved_session . ", $tmp markers";
$markers = $_SESSION['clicked_buttons'];
} else {
if ($message2 == "") {
$message1 = "0 markers ";
$message2 = "for all markers.";
} else {
$message1 = $message1 . ", 0 markers ";
$message2 = $message2 . " for all markers";
}
}
$this->refreshTitle();
if (empty($_SESSION['phenotype'])) {
echo "<font color=red>Select a set of traits and phenotype trials</font><br><br>";
} elseif (empty($_SESSION['selected_lines'])) {
echo "<br>Select validation set containing trait measurements to plot prediction vs observed. ";
echo "<a href=";
echo $config['base_url'];
echo "downloads/select_all.php>Wizard</a><br>";
echo "Select prediction set without trait measurements to predict the traits. ";
echo "<a href=";
echo $config['base_url'];
echo "pedigree/line_properties.php>Lines by Properties</a>, ";
echo "<a href=";
echo $config['base_url'];
echo "downloads/select_genotype.php>Lines by Genotype Experiment</a><br>";
} elseif (empty($_SESSION['phenotype']) && empty($_SESSION['training_traits'])) {
echo "Please select traits before using this feature.<br><br>";
echo "<a href=";
echo $config['base_url'];
echo "phenotype/phenotype_selection.php>Select Traits</a><br><br>";
echo "<a href=";
echo $config['base_url'];
echo "downloads/select_all.php>Wizard (Lines, Traits, Trials)</a>";
} elseif (empty($_SESSION['selected_map'])) {
if (isset($_SESSION['geno_exps'])) {
$geno_exp = $_SESSION['geno_exps'];
$geno_str = $geno_exp[0];
$sql = "select marker_uid from allele_bymarker_exp_101 where experiment_uid = $geno_str and pos is not null limit 10";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli) . $sql);
if ($row = mysqli_fetch_array($res)) {
} else {
echo "<font color=red>Select a genetic map.</font>";
echo "<input type=button value=\"Genetic map\" onclick=\"javascript: select_map()\"><br>";
}
} else {
echo "<font color=red>Select a genetic map.</font>";
echo "<input type=button value=\"Genetic map\" onclick=\"javascript: select_map()\"><br>";
}
}
if (!empty($_SESSION['training_lines']) && !empty($_SESSION['selected_lines'])) {
if (empty($_SESSION['selected_trials'])) {
echo "<tr><td>Prediction<td>";
} else {
echo "<tr><td>Validation<td>";
$tmp = $_SESSION['selected_trials'];
$e_uid = implode(",", $tmp);
$sql = "select trial_code from experiments where experiment_uid IN ($e_uid)";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli) . $sql);
while ($row = mysqli_fetch_array($res)) {
echo "$row[0]<br>";
}
}
$count = count($_SESSION['selected_lines']);
$markers = $_SESSION['filtered_markers'];
$estimate = count($markers) + count($lines);
echo "<td>$count";
?>
<td>
<form method="LINK" action="gensel.php">
<input type="hidden" value="step1gensel" name="function">
<input type="hidden" value="clear_p" name="cmd">
<input type="submit" value="Clear Selection">
</form>
<?php
//check if these are unique
$count = 0;
$count_dup = 0;
$tmp1 = $_SESSION['training_lines'];
$tmp2 = $_SESSION['selected_lines'];
$count_t = count($tmp2);
foreach ($tmp2 as $uid) {
if (in_array($uid, $tmp1)) {
$count_dup++;
} else {
$count++;
}
}
if ($count < 5) {
echo " <font color=red>(Error - $count unique lines in prediction set)";
}
}
echo "</table>";
if ($count_dup > 0) {
if (empty($_SESSION['selected_trials'])) {
echo " Warning - $count_dup lines removed from prediction set because they are in training set";
} else {
echo " Warning - $count_dup lines removed from validation set because they are in training set";
}
}
$min_maf = 5;
$max_missing = 10;
$max_miss_line = 10;
$unique_str = chr(rand(65, 80)).chr(rand(65, 80)).chr(rand(65, 80)).chr(rand(65, 80));
?>
</div>
<?php
if (!empty($_SESSION['training_lines']) && !empty($_SESSION['selected_lines'])) {
$min_maf = 5;
$max_missing = 10;
$max_miss_line = 10;
$unique_str = chr(rand(65, 80)).chr(rand(65, 80)).chr(rand(65, 80)).chr(rand(65, 80));
?>
<p>Minimum MAF ≥ <input type="text" name="mmaf" id="mmaf" size="2" value="<?php echo ($min_maf) ?>" />%
Remove markers missing > <input type="text" name="mmm" id="mmm" size="2" value="<?php echo ($max_missing) ?>" />% of data
Remove lines missing > <input type="text" name="mml" id="mml" size="2" value="<?php echo ($max_miss_line) ?>" />% of data
<div id="filter" style="clear: both; float: left; margin-bottom: 1.5em; width: 100%"></div>
<div id="step1" style="clear: both; float: left; margin-bottom: 1.5em; width: 100%">
<img alt="spinner" id="spinner" src="images/ajax-loader.gif" style="display:none;" /></div>
<div id="step2" style="clear: both; float: left; margin-bottom: 1.5em; width: 100%">
<table>
<!--tr><td><td>fixed effect (trial is always included)-->
<tr><td><input type="button" value="G-BLUP Analysis" onclick="javascript:load_genomic_prediction(<?php echo $estimate; ?>)">
<!-td-->
</table><br>
</div>
<div id="step3" style="clear: both; float: left; margin-bottom: 1.5em; width: 100%"></div>
<div id="step4" style="clear: both; float: left; margin-bottom: 1.5em; width: 100%"></div>
<div id="step5" style="clear: both; float: left; margin-bottom: 1.5em; width: 100%">
<?php
echo "</div>";
}
echo "</div>";
}
/**
* filters markers and lines based on settings
*/
private function filterLines()
{
if (isset($_GET['maf'])) {
$min_maf = $_GET['maf'];
} else {
$min_maf = 5;
}
if (isset($_GET['mmm'])) {
$max_missing = $_GET['mmm'];
} else {
$max_missing = 10;
}
if (isset($_GET['mml'])) {
$max_miss_line = $_GET['mml'];
} else {
$max_miss_line = 10;
}
$lines = $_SESSION['selected_lines'];
if (isset($_SESSION['training_lines'])) {
$training_lines = $_SESSION['training_lines'];
} else {
$training_lines = "";
}
if (isset($_SESSION['geno_exps'])) {
$experiment_uid = $_SESSION['geno_exps'][0];
calculate_afe($experiment_uid, $min_maf, $max_missing, $max_miss_line);
findCommonLines($lines);
} elseif ($training_lines == "") {
calculate_af($lines, $min_maf, $max_missing, $max_miss_line);
} else {
calculate_af($training_lines, $min_maf, $max_missing, $max_miss_line);
}
?>
<img alt="spinner" id="spinner" src="images/ajax-loader.gif" style="display:none;" />
<?php
}
/**
* 1. display a spinning activity image when a slow function is running
* 2. show button to clear sessin data
* 3. show button to save current selection
*/
private function refreshTitle()
{
global $mysqli;
$command = (isset($_GET['cmd']) && !empty($_GET['cmd'])) ? $_GET['cmd'] : null;
echo "<h2>Genomic Association and Prediction</h2>";
if (!empty($_SESSION['training_traits'])) {
$tmp = $_SESSION['training_traits'];
$tmp = $tmp[0];
$sql = "select phenotypes_name from phenotypes where phenotype_uid = '$tmp'";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
$row = mysqli_fetch_array($res);
echo "<h3>Trait: $row[0]</h3>";
}
if ($command == "save_t") {
if (!empty($_SESSION['selected_traits'])) {
$_SESSION['training_traits'] = $_SESSION['selected_traits'];
$_SESSION['training_trials'] = $_SESSION['selected_trials'];
$_SESSION['training_lines'] = $_SESSION['selected_lines'];
unset($_SESSION['selected_trials']);
unset($_SESSION['selected_lines']);
unset($_SESSION['filtered_lines']);
unset($_SESSION['filtered_markers']);
unset($_SESSION['clicked_buttons']);
} else {
echo "error - no selection found";
}
} elseif ($command == "save_p") {
$_SESSION['predict_traits'] = $_SESSION['selected_traits'];
$_SESSION['predict_trials'] = $_SESSION['selected_trials'];
$_SESSION['predict_lines'] = $_SESSION['selected_lines'];
} elseif ($command == "clear") {
unset($_SESSION['selected_traits']);
unset($_SESSION['selected_trials']);
unset($_SESSION['selected_lines']);
unset($_SESSION['training_traits']);
unset($_SESSION['training_trials']);
unset($_SESSION['training_lines']);
unset($_SESSION['filtered_lines']);
unset($_SESSION['phenotype']);
} elseif ($command== "clear_p") {
unset($_SESSION['selected_traits']);
unset($_SESSION['selected_trials']);
unset($_SESSION['selected_lines']);
}
if (empty($_SESSION['selected_lines']) || empty($_SESSION['training_lines'])) {
?>
<table>
<tr><td><b>Genome Wide Association (consensus genotype)</b><br>
1. Select a <a href="downloads/select_all.php">set of lines, trait, and trials</a> (one trait).<br>
2. Select the <a href="maps/select_map.php">genetic map</a> which has the best coverage for this set.<br>
3. Return to this page and select model options then GWAS Analysis<br>
<td><b>Genome Wide Association (single genotype experiment)</b><br>
1. Select a <a href="downloads/select_genotype.php">set of lines by genotype experiment</a>.<br>
2. Select a <a href="phenotype/phenotype_selection.php">trait and phenotype trial</a>.<br>
3. Select the <a href="maps/select_map.php">genetic map</a> which has the best coverage for this set.<br>
4. Return to this page and select model options then GWAS Analysis<br>
<tr><td colspan=2><b>Genomic Prediction</b><br>
1. Select a <a href="downloads/select_all.php">set of lines, trait, and trials</a> (one trait).<br>
2. Return to this page and select G-BLUP Analysis for cross-validation of the training set. Then save Training Set.<br>
3. To select a validation set, select a new set of lines using a different trial, then return to this page for analysis.<br>
4. To select a prediction set, select a new set of lines without phenotype measurements, then return to this page for analysis.<br>
</table>
<p><a href="downloads/genomic-tools.php">Additional notes on GWAS and G-BLUP methods</a><br>
<?php
}
if (!empty($_SESSION['training_traits']) && !empty($_SESSION['training_trials'])) {
echo "<table>";
echo "<tr><td>Set<td>Trials<td>Lines<td>";
$p_uid = $_SESSION['training_traits'];
$p_uid = $p_uid[0];
$sql = "select phenotypes_name from phenotypes where phenotype_uid = $p_uid";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
$row = mysqli_fetch_array($res);
echo "<tr><td>Training<td>";
if (!empty($_SESSION['training_trials'])) {
$tmp = $_SESSION['training_trials'];
$e_uid = implode(",",$tmp);
$sql = "select trial_code from experiments where experiment_uid IN ($e_uid)";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
while ($row = mysqli_fetch_array($res)) {
echo "$row[0]<br>";
}
}
echo "<td>";
if (count($_SESSION['training_lines']) > 0) {
$selectedlines = implode(",", $_SESSION['training_lines']);
$sql_option = " AND lr.line_record_uid IN ($selectedlines)";
} else {
$sql_option = "";
}
$sql = "SELECT count(DISTINCT lr.line_record_uid)
FROM tht_base as tb, phenotype_data as pd, phenotypes as p, line_records as lr
WHERE pd.tht_base_uid = tb.tht_base_uid
$sql_option
AND p.phenotype_uid = pd.phenotype_uid
AND lr.line_record_uid = tb.line_record_uid
AND pd.phenotype_uid = $p_uid
AND tb.experiment_uid IN ($e_uid)";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
$row = mysqli_fetch_array($res);
echo "$row[0]";
?>
<td>
<form method="LINK" action="gensel.php">
<input type="hidden" value="step1gensel" name="function">
<input type="hidden" value="clear" name="cmd">
<input type="submit" value="Clear Selection">
</form>
<?php
if (empty($_SESSION['selected_lines'])) {
echo "</table>";
}
} elseif (!empty($_SESSION['phenotype']) && !empty($_SESSION['selected_trials']) ) {
?>
<table>
<tr><td>Traits<td>Trials<td>Lines<td>Genetic Map
<tr><td>
<?php
$traits = $_SESSION['phenotype'];
$map = $_SESSION['selected_map'];
//$traits= implode(",",$tmp); use when I get this working for multiple traits
$sql = "select phenotypes_name from phenotypes where phenotype_uid IN ($traits)";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
while ($row = mysqli_fetch_array($res)) {
echo "$row[0]<br>";
}
echo "<td>";
$tmp = $_SESSION['selected_trials'];
$e_uid = implode(",",$tmp);
$sql = "select trial_code from experiments where experiment_uid IN ($e_uid)";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
while ($row = mysqli_fetch_array($res)) {
echo "$row[0]<br>";
}
echo "<td>";
$count = count($_SESSION['selected_lines']);
echo "$count<td>";
if (isset($_SESSION['geno_exps'])) {
$geno_exp = $_SESSION['geno_exps'];
$geno_str = $geno_exp[0];
$sql = "select marker_uid from allele_bymarker_exp_101 where experiment_uid = $geno_str and pos is not null limit 10";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
if ($row = mysqli_fetch_array($res)) {
$sql = "select trial_code from experiments where experiment_uid = $geno_str";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
$row = mysqli_fetch_array($res);
$name = $row[0];
echo "using map from genotype experiment<br>$name";
} elseif (isset($_SESSION['selected_map'])) {
$sql = "select mapset_name from mapset where mapset_uid = $map";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
$row = mysqli_fetch_assoc($res);
$map_name = $row['mapset_name'];
echo "$map_name";
}
} elseif (isset($_SESSION['selected_map'])) {
$sql = "select mapset_name from mapset where mapset_uid = $map";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
$row = mysqli_fetch_assoc($res);
$map_name = $row['mapset_name'];
echo "$map_name";
}
echo "</table>";
if ($count < 10) {
echo "<font color=red>Warning: analysis may fail with only $count lines selected</font><td>";
}
$min_maf = 5;
$max_missing = 10;
$max_miss_line = 10;
$lines = $_SESSION['selected_lines'];
$count_markers = calculate_db($lines, $min_maf, $max_missing, $max_miss_line);
$count_lines = count($lines);
$estimate = ($count_markers * $count_lines) / 10000;
if ($count > 0) {
?>
<br><table><tr><td>Minimum MAF ≥ <input type="text" name="mmaf" id="mmaf" size="2" value="<?php echo ($min_maf) ?>" /><br>
Remove markers missing > <input type="text" name="mmm" id="mmm" size="2" value="<?php echo ($max_missing) ?>" />% of data<br>
<?php
if (!isset($_SESSION['geno_exps'])) {
?>
Remove lines missing > <input type="text" name="mml" id="mml" size="2" value="<?php echo ($max_miss_line) ?>" />% of data<br>
<?php
} else {
?>
<input type="hidden" name="mml" id="mml">
<?php
}
if (isset($_SESSION['outliers'])) {
?>
Remove trait outliers <input type="checkbox" id="removeOutlier" value="Y">
<?php
}
?>
<td><input type="button" value="Filter Lines and Markers" onclick="javascript:filter_lines();"/>
</table>
</div>
<div id="filter" style="clear: both; float: left; margin-bottom: 1.5em; width: 100%">
<img alt="spinner" id="spinner" src="images/ajax-loader.gif" style="display:none;" /></div>
<div id="step1" style="clear: both; float: left; margin-bottom: 1.5em; width: 100%"></div>
<div id="step2" style="clear: both; float: left; margin-bottom: 1.5em; width: 100%">
<table border=0>
<tr><td rowspan=2>
<input type="button" value="Analyze" onclick="javascript:load_genomic_gwas(<?php echo $estimate; ?>)"> GWAS
<td>principal components
<td><select name="model2" onchange="javascript: update_fixed(this.value)">
<option>0</option>
<option>1</option>
<option>2</option>
<option>3</option>
<option>4</option>
<option>5</option>
</select>
<tr><td>method
<td><input type="radio" name="P3D" checked value="TRUE">EMMAX (faster but can underestimate significance)<br>
<input type="radio" name="P3D" value="FALSE">EMMA with REML
<tr><td><input type="button" value="Analyze" onclick="javascript:load_genomic_prediction('<?php echo $estimate; ?>')"> G-BLUP
<td>
</table><br>
<form action="gensel.php">
<input type="hidden" value="step1gensel" name="function">
<input type="hidden" value="save_t" name="cmd">
<input type="submit" value="Save Training Set">
then continue to select prediction set
</form>
</div>
<div id="step3" style="clear: both; float: left; margin-bottom: 1.5em; width: 100%"></div>
<div id="step4" style="clear: both; float: left; margin-bottom: 1.5em; width: 100%"></div>
<div id="step5" style="clear: both; float: left; margin-bottom: 1.5em; width: 100%">
<?php
} else {
echo "<font color=red>Warning, not a valid combination of traits, trials, and lines</font>";
}
}
?>
</p>
<?php
}
/**
* setup results page for R stat analysis
*/
private function genomic_prediction() {
?>
<h2>Genomic Selection</h2>
<img alt="spinner" id="spinner" src="images/ajax-loader.gif" style="display:none;" />
<?php
}
/**
* call R program for displaying histograms
*/
private function run_histo() {
global $mysqli;
$unique_str = $_GET['unq'];
$dir = '/tmp/tht/';
$filename1 = 'THTdownload_hapmap_' . $unique_str . '.txt';
$filename2 = 'THTdownload_traits_' . $unique_str . '.txt';
$filename3 = 'THTdownload_histo_' . $unique_str . '.R';
$filename4 = 'THTdownload_histo_' . $unique_str . '.png';
$filename5 = 'process_error_histo_' . $unique_str . '.txt';
if (isset($_SESSION['training_traits'])) {
$phenotype = $_SESSION['training_traits'];
$phenotype = $phenotype[0];
} elseif (isset($_SESSION['selected_traits'])) {
$phenotype = $_SESSION['selected_traits'];
$phenotype = $phenotype[0];
}
$sql = "select phenotypes_name, unit_name from phenotypes, units
where phenotypes.unit_uid = units.unit_uid
and phenotype_uid = $phenotype";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
$row = mysqli_fetch_array($res);
$phenolabel = $row[0];
$phenounit = $row[1];
$ntrials = 0;
$triallabel = "";
if (isset($_SESSION['selected_trials'])) {
$trials = $_SESSION['selected_trials'];
foreach ($trials as $uid) {
$sql = "select trial_code from experiments where experiment_uid = $uid";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
if ($row = mysqli_fetch_array($res)) {
$trial = $row[0];
}
if ($triallabel == "") {
$triallabel = "triallabel <- list()\n";
}
$triallabel .= "triallabel[$uid] <- \"$trial\"\n";
$ntrials++;
}
}
if (isset($_SESSION['training_trials'])) {
$trials = $_SESSION['training_trials'];
foreach ($trials as $uid) {
$sql = "select trial_code from experiments where experiment_uid = $uid";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
if ($row = mysqli_fetch_array($res)) {
$trial = $row[0];
}
if ($triallabel == "") {
$triallabel= "triallabel <- list()\n";
}
$triallabel .= "triallabel[$uid] <- \"$trial\"\n";
$ntrials++;
}
}
$histo_width = 800;
if ($ntrials > 3) {
$histo_width = 800 + ($ntrials - 3) * 200;
}
if(!file_exists($dir.$filename3)){
$h = fopen($dir.$filename3, "w+");
$png = "png(\"$dir$filename4\", width=$histo_width, height=300)\n";
$cmd1 = "phenoData <- as.matrix(read.delim(\"$dir$filename2\", header=TRUE, na.strings=\"-999\", stringsAsFactors=FALSE, sep=\"\\t\", row.names=1))\n";
$cmd1 = "phenoData <- read.table(\"$dir$filename2\", header=TRUE, na.strings=\"-999\", stringsAsFactors=FALSE, sep=\"\\t\", row.names=NULL)\n";
$cmd2 = "phenolabel <- \"$phenolabel\"\n";
$cmd3 = "phenounit <- \"$phenounit\"\n";
$cmd4 = $triallabel;
fwrite($h, $png);
fwrite($h, $cmd1);
fwrite($h, $cmd2);
fwrite($h, $cmd3);
fwrite($h, $cmd4);
fclose($h);
}
exec("cat /tmp/tht/$filename3 R/GShisto.R | R --vanilla > /dev/null 2> /tmp/tht/$filename5");
if (file_exists("/tmp/tht/$filename5")) {
$h = fopen("/tmp/tht/$filename5", "r");
while ($line=fgets($h)) {
echo "$line<br>\n";
}
fclose($h);
}
if (file_exists("/tmp/tht/$filename4")) {
print "<img src=\"/tmp/tht/$filename4\" /><br>";
} else {
echo "Error in R script R/GShisto.R<br>\n";
}
}
private function display_gwas_hits($h) {
global $mysqli;
echo "Top five marker scores from GWAS analysis<br>";
echo "<table><tr><td>marker<td>chrom<td>pos<td>value<td>external link (resource name)";
$line= fgetcsv($h);
while ($line= fgetcsv($h)) {
$link = "";
$sql = "select value, name_annotation, linkout_string_for_annotation
from markers, marker_annotations, marker_annotation_types
where markers.marker_uid = marker_annotations.marker_uid
and marker_annotations.marker_annotation_type_uid = marker_annotation_types.marker_annotation_type_uid
and marker_name = \"$line[1]\"";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
while ($row = mysqli_fetch_assoc($res)) {
$reg_pattern = '/XXXX/';
$replace_string = $row['value'];
$name = $row['name_annotation'];
$source_string = $row['linkout_string_for_annotation'];
$linkString = preg_replace($reg_pattern, $replace_string, $source_string);
if ($link == "") {
if ($linkString != "") {
$link = "<a href=\"$linkString\" target=\"_new\">$replace_string</a> ($name)";
}
} else {
if ($linkString != "") {
$link .= "<br><a href=\"$linkString\" target=\"_new\">$replace_string</a> ($name)";
}
}
}
if ($count < 5) {
$markerlink = "<a href=$config[base_url]view.php?table=markers&name=$line[1]>$line[1]</a>";
echo "<tr><td>$markerlink<td>$line[2]<td>$line[3]<td>$line[4]<td>$link\n";
}
$count++;
}
fclose($h);
echo "</table>";
}
/**
* display gwas results
*/
private function status_gwas() {
$unique_str = $_GET['unq'];
$dir = '/tmp/tht/';
$found = 1;
$filename9 = 'THTdownload_hmp_' . $unique_str. '.txt';
$filename2 = 'THTdownload_traits_' . $unique_str . '.txt';
$filename3 = 'THTdownload_gwa_' . $unique_str . '.R';
$filename4 = 'THTdownload_gwa1_' . $unique_str . '.png';
$filename7 = 'THTdownload_gwa2_' . $unique_str . '.png';
$filename10 = 'THTdownload_gwa3_' . $unique_str . '.png';
$filename5 = 'process_error_gwa_' . $unique_str . '.txt';
$filename6 = 'R_error_gwa_' . $unique_str . '.txt';
$filename1 = 'THT_result_' . $unique_str . '.csv';
$filenameK = 'Kinship_matrix_' . $unique_str . '.csv';
if (file_exists("/tmp/tht/$filename7")) {
} else {
//echo "$filename7 not ready<br>\n";
$found = 0;
}
if (file_exists("/tmp/tht/$filename10")) {
} else {
//echo "$filename10 not ready<br>\n";
$found = 0;
}
if (file_exists("/tmp/tht/$filename4")) {
} else {
//echo "$filename4 not ready<br>\n";
$found = 0;
}
if (file_exists("/tmp/tht/$filename5")) {
$h = fopen("/tmp/tht/$filename5", "r");
while ($line=fgets($h)) {
echo "$line<br>\n";
}
fclose($h);
}
if (file_exists("/tmp/tht/$filename3")) {
// Extract the Trait name from the .R file.
$h = fopen("/tmp/tht/$filename3", "r");
while ($line=fgets($h)) {
if (strpos($line, 'phenolabel') !== FALSE) {
$traitname = preg_replace('/phenolabel <- "(.*)"/', '$1', $line);
}
}
fclose($h);
}
if ($found) {
print "<img src=\"/tmp/tht/$filename7\" width=\"800\"/><br>";
print "<img src=\"/tmp/tht/$filename10\" width=\"800\"/><br>";
print "<img src=\"/tmp/tht/$filename4\" width=\"800\" /><br>";
print "Trait: <b>$traitname</b><p>";
print "<a href=/tmp/tht/$filename1 target=\"_blank\" type=\"text/csv\">Export GWAS results to CSV file</a> ";
print "with columns for marker name, chromosome, position, marker score<br><br>";
print "<a href=/tmp/tht/$filenameK target=\"_blank\" type=\"text/csv\">Export Kinship matrix</a><br><br>";
$count = 0;
$h = fopen("/tmp/tht/$filename1", "r");
if ($h) {
$this->display_gwas_hits($h);
}
} else {
if (isset($_SESSION['filtered_ines'])) {
$lines = $_SESSION['filtered_lines'];
} else {
$lines = $_SESSION['selected_lines'];
}
if (isset($_SESSION['filtered_markers'])) {
$markers = $_SESSION['filtered_markers'];
} else {
$markers = $_SESSION['geno_exps_cnt'];
}
$estimate = count($lines) * count($markers);
$estimate = round($estimate/6000000,1);
echo "Results not ready yet. Estimated analysis time is $estimate minutes using default options.<br>";
?>
<font color=red>Select the "Check Results" button to retrieve results.<br>
<input type="button" value="Check Results" onclick="javascript: run_status('<?php echo $unique_str; ?>');"/>
</font>
<?php
}
}
/**
* display genomic prediction results
*/
private function status_pred() {
$unique_str = $_GET['unq'];
$dir = '/tmp/tht/';
$found = 1;
$filename1 = 'THTdownload_hapmap_' . $unique_str . '.txt';
$filename2 = 'THTdownload_traits_' . $unique_str . '.txt';
$filename3 = 'THTdownload_gensel_' . $unique_str . '.R';
$filename10 = 'THTdownload_gensel2_' . $unique_str . '.png';
$filename4 = 'THTdownload_gensel_' . $unique_str . '.png';
$filename5 = 'THT_process_error_' . $unique_str . '.txt';
$filename6 = 'THT_R_error_' . $unique_str . '.txt';
$filename7 = 'THT_result_' . $unique_str . '.csv';
if (file_exists("/tmp/tht/$filename10")) {
print "<img src=\"/tmp/tht/$filename10\" /><br>";
} else {
$found = 0;
}
if (file_exists("/tmp/tht/$filename4")) {
print "<img src=\"/tmp/tht/$filename4\" /><br>";
if (isset($_SESSION['selected_trials'])) {
print "<a href=/tmp/tht/$filename7 target=\"_blank\" type=\"text/csv\">Export prediction to CSV file</a><br><br>";
} else {
print "Cross-validation of training set using 5 folds and 2 repeats.<br>\n";
print "<a href=/tmp/tht/$filename7 target=\"_blank\" type=\"text/csv\">Export Cross-validated prediction to CSV file</a><br><br>";
}
} else {
$found = 0;
}
if (file_exists("/tmp/tht/$filename5")) {
$h = fopen("/tmp/tht/$filename5", "r");
while ($line=fgets($h)) {
echo "$line<br>\n";
}
fclose($h);
}
if (file_exists("/tmp/tht/$filename6")) {
$h = fopen("/tmp/tht/$filename6", "r");
while ($line=fgets($h)) {
echo "$line<br>\n";
}
fclose($h);
}
if ($found == 0) {
$lines = $_SESSION['filtered_lines'];
$markers = $_SESSION['filtered_markers'];
$estimate = count($lines) + count($markers);
$estimate = round($estimate/700,1);
echo "Results not ready yet. Estimated analysis time is $estimate minutes.<br>";
?>
<font color=red>Select the "Check Results" button to retrieve results.<br>
<input type="button" value="Check Results" onclick="javascript: run_status('<?php echo $unique_str; ?>');"/>
</font>
<?php
}
}
/**
* display results from GWAS
*/
private function run_gwa() {
global $mysqli;
$unique_str = $_GET['unq'];
$model_opt = $_GET['fixed2'];
$p3d = $_GET['p3d'];
if (isset($_SESSION['training_traits'])) {
$phenotype = $_SESSION['training_traits'];
$phenotype = $phenotype[0];
//} elseif (isset($_SESSION['selected_traits'])) { use when multiple traits is working
} elseif (isset($_SESSION['phenotype'])) {
$phenotype = $_SESSION['phenotype'];
}
$sql = "select phenotypes_name, unit_name from phenotypes, units
where phenotypes.unit_uid = units.unit_uid
and phenotype_uid = $phenotype";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
$row = mysqli_fetch_array($res);
$phenolabel = $row[0];
//$unique_fld = chr(rand(65,80)).chr(rand(65,80)).chr(rand(65,80)).chr(rand(65,80));
//mkdir("/tmp/tht/$unique_fld"); it would be better to put all files in directory
$dir = '/tmp/tht/';
$filename9 = 'THTdownload_hmp_' . $unique_str. '.txt';
$filename2 = 'THTdownload_traits_' . $unique_str . '.txt';
$filename3 = 'THTdownload_gwa_' . $unique_str . '.R';
$filename4 = 'THTdownload_gwa1_' . $unique_str . '.png';
$filename7 = 'THTdownload_gwa2_' . $unique_str . '.png';
$filename10 = 'THTdownload_gwa3_' . $unique_str . '.png';
$filename5 = 'process_error_gwa_' . $unique_str . '.txt';
$filename6 = 'R_error_gwa_' . $unique_str . '.txt';
$filename1 = 'THT_result_' . $unique_str . '.csv';
$filenameK = 'Kinship_matrix_' . $unique_str . '.csv';
if(!file_exists($dir.$filename3)){
$h = fopen($dir.$filename3, "w+");
$png1 = "png(\"$dir$filename4\", width=1200, height=400)\n";
$png2 = "png(\"$dir$filename7\", width=1200, height=400)\n";
$png3 = "png(\"$dir$filename10\", width=1200, height=400)\n";
$png4 = "dev.set(3)\n";
$cmd3 = "phenoData <- read.table(\"$dir$filename2\", header=TRUE, na.strings=\"-999\", stringsAsFactors=FALSE, sep=\"\\t\", row.names=NULL)\n";
$cmd4 = "hmpData <- read.table(\"$dir$filename9\", header=TRUE, stringsAsFactors=FALSE, sep=\"\\t\", check.names = FALSE)\n";
$cmd5 = "phenolabel <- \"$phenolabel\"\n";
$cmd6 = "fileerr <- \"$dir$filename6\"\n";
$cmd7 = "fileout <- \"$filename1\"\n";
$cmd8 = "model_opt <- \"$model_opt\"\n";
$cmd9 = "fileK <- \"$filenameK\"\n";
fwrite($h, $png1);
fwrite($h, $png2);
fwrite($h, $png3);
fwrite($h, $png4);
fwrite($h, $cmd3);
fwrite($h, $cmd4);
fwrite($h, $cmd5);
fwrite($h, $cmd6);
fwrite($h, $cmd7);
fwrite($h, $cmd8);
fwrite($h, $cmd9);
fwrite($h, "p3d <- $p3d\n");
fwrite($h, "setwd(\"/tmp/tht/\")\n");
fclose($h);
}
exec("cat /tmp/tht/$filename3 R/GSforGWA.R | R --vanilla > /dev/null 2> /tmp/tht/$filename5");
if (file_exists("/tmp/tht/$filename7")) {
print "<img src=\"/tmp/tht/$filename7\" width=\"800\" /><br>";
} else {
echo "Error in R script<br>\n";
echo "cat /tmp/tht/$filename3 R/GSforT3.R | R --vanilla <br>";
}
if (file_exists("/tmp/tht/$filename10")) {
print "<img src=\"/tmp/tht/$filename10\" width=\"800\"/><br>";
}
if (file_exists("/tmp/tht/$filename4")) {
print "<img src=\"/tmp/tht/$filename4\" width=\"800\" /><br>";
print "Trait: $phenolabel<p>";
print "<a href=/tmp/tht/$filename1 target=\"_blank\" type=\"text/csv\">Export GWAS results to CSV file</a> ";
print "with columns for marker name, chromosome, position, marker score<br><br>";
print "<a href=/tmp/tht/$filenameK target=\"_blank\" type=\"text/csv\">Export Kinship matrix</a><br><br>";
$count = 0;
$h = fopen("/tmp/tht/$filename1", "r");
if($h) {
$this->display_gwas_hits($h);
} else {
echo "error - could not open $filename1\n";
}
}
if (file_exists("/tmp/tht/$filename5")) {
$h = fopen("/tmp/tht/$filename5", "r");
while ($line=fgets($h)) {
echo "$line<br>\n";
}
fclose($h);
}
}
/**
* run GWAS results in background and notify when complete
*/
private function run_gwa2() {
global $config;
global $mysqli;
$unique_str = $_GET['unq'];
$model_opt = $_GET['fixed2'];
$p3d = $_GET['p3d'];
if (isset($_SESSION['training_traits'])) {
$phenotype = $_SESSION['training_traits'];
$phenotype = $phenotype[0];
//} elseif (isset($_SESSION['selected_traits'])) { use when multiple traits is working
} elseif (isset($_SESSION['phenotype'])) {
$phenotype = $_SESSION['phenotype'];
}
$sql = "select phenotypes_name, unit_name from phenotypes, units
where phenotypes.unit_uid = units.unit_uid
and phenotype_uid = $phenotype";
$res = mysqli_query($mysqli, $sql) or die(mysqli_error($mysqli));
$row = mysqli_fetch_array($res);
$phenolabel = $row[0];
//$unique_fld = chr(rand(65,80)).chr(rand(65,80)).chr(rand(65,80)).chr(rand(65,80));
//mkdir("/tmp/tht/$unique_fld"); it would be better to put all files in directory
$dir = '/tmp/tht/';
$filename9 = 'THTdownload_hmp_' . $unique_str. '.txt';
$filename2 = 'THTdownload_traits_' . $unique_str . '.txt';
$filename3 = 'THTdownload_gwa_' . $unique_str . '.R';
$filename4 = 'THTdownload_gwa1_' . $unique_str . '.png';
$filename7 = 'THTdownload_gwa2_' . $unique_str . '.png';
$filename10 = 'THTdownload_gwa3_' . $unique_str . '.png';
$filename5 = 'process_error_gwa_' . $unique_str . '.txt';
$filename6 = 'R_error_gwa_' . $unique_str . '.txt';
$filename1 = 'THT_result_' . $unique_str . '.csv';
$filenameK = 'Kinship_matrix_' . $unique_str . '.csv';
if(!file_exists($dir.$filename3)){
$h = fopen($dir.$filename3, "w+");
$png1 = "png(\"$dir$filename4\", width=1200, height=400)\n";
$png2 = "png(\"$dir$filename7\", width=1200, height=400)\n";
$png3 = "png(\"$dir$filename10\", width=1200, height=400)\n";
$png4 = "dev.set(3)\n";
$cmd3 = "phenoData <- read.table(\"$dir$filename2\", header=TRUE, na.strings=\"-999\", stringsAsFactors=FALSE, sep=\"\\t\", row.names=NULL)\n";
$cmd4 = "hmpData <- read.table(\"$dir$filename9\", header=TRUE, stringsAsFactors=FALSE, sep=\"\\t\", check.names = FALSE)\n";
$cmd5 = "phenolabel <- \"$phenolabel\"\n";
$cmd6 = "fileerr <- \"$dir$filename6\"\n";
$cmd7 = "fileout <- \"$filename1\"\n";
$cmd8 = "model_opt <- \"$model_opt\"\n";
$cmd9 = "fileK <- \"$filenameK\"\n";
if (isset($_SESSION['username'])) {
$emailAddr = $_SESSION['username'];
$emailAddr = "email <- \"$emailAddr\"\n";