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blastresult.php
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<?php
#######################################################################################
# ViroBLAST
# blastresult.php
# Copyright © University of Washington. All rights reserved.
# Written by Wenjie Deng in the Department of Microbiology at University of Washington.
#######################################################################################
?>
<!DOCTYPE html>
<html>
<head><title>ViroBLAST Result Page</title>
<link href="stylesheets/viroblast.css" rel="Stylesheet" type="text/css" />
<script type="text/javascript" src='javascripts/sorttable.js'></script>
<script type="text/javascript">
function checkform(form) {
var checkbox_checked = 0;
if (form.dldseq.checked) {
checkbox_checked++;
}else {
for (var i = 0; i < form.checkedSeq.length; i++) {
if (form.checkedSeq[i].checked) {
checkbox_checked++;
break;
}
}
}
if (checkbox_checked == 0) {
alert ("Please check the sequence(s) you want to download");
return false;
}
return true;
}
</script>
</head>
<body>
<div id="header">
<div class="spacer"> </div>
<span class="logo"><a name="top"></a>ViroBLAST Result</span>
</div>
<div id="nav">
<span class='nav'><a href="viroblast.php" class="nav">Home</a></span>
<span class='nav'><a href=docs/aboutviroblast.html class="nav">About ViroBLAST</a></span>
<span class='nav'><a href=docs/viroblasthelp.html class="nav">Help</a></span>
</div>
<div class="spacer"> </div>
<div id="indent">
<?php
include("include/path.inc");
$jobid = (empty($_GET['jobid'])) ? '' : $_GET['jobid'];
$blastdb = (empty($_POST['blastdb'])) ? '' : $_POST['blastdb'];
$blastpath = (empty($_POST['blastpath'])) ? '' : $_POST['blastpath'];
$patientIDarray = (empty($_POST['patientIDarray'])) ? '' : $_POST['patientIDarray'];
$opt = (empty($_GET['opt'])) ? '' : $_GET['opt'];
$blast_flag = (empty($_POST['blast_flag'])) ? '' : $_POST['blast_flag'];
$filter_flag = (empty($_POST['filter_flag'])) ? '' : $_POST['filter_flag'];
$filt_val = (empty($_POST['filt_val'])) ? '' : $_POST['filt_val'];
$cutoffType = (empty($_POST['cutoffType'])) ? '' : $_POST['cutoffType'];
$pct_cutoff = (empty($_POST['pct_cutoff'])) ? '' : $_POST['pct_cutoff'];
$blst_cutoff = (empty($_POST['blst_cutoff'])) ? '' : $_POST['blst_cutoff'];
$searchType = (empty($_POST['searchType'])) ? '' : $_POST['searchType'];
$program = (empty($_POST['program'])) ? '' : $_POST['program'];
$dot = (empty($_GET['dot'])) ? '' : $_GET['dot'];
$querySeq = (empty($_POST['querySeq'])) ? '' : $_POST['querySeq'];
$blastagainstfile = (empty($_FILES['blastagainstfile']['name'])) ? '' : $_FILES['blastagainstfile']['name'];
$alignmentView = (empty($_GET['alignmentView'])) ? '' : $_GET['alignmentView'];
if ($blast_flag == 1) {
$jobid = time().rand(10, 99);
}
if (!$blast_flag && !$jobid) {
echo "<p>Error: No job submitted.</p>";
footer();
exit;
}
if ($searchType == 'advanced') {
$expect=(empty($_POST['expect'])) ? 10 : $_POST['expect'];
$wordSize = (empty($_POST['wordSize'])) ? '' : $_POST['wordSize'];
$targetSeqs = (empty($_POST['targetSeqs'])) ? '' : $_POST['targetSeqs'];
$mmScore = (empty($_POST['mmScore'])) ? '' : $_POST['mmScore'];
$matrix = (empty($_POST['matrix'])) ? '' : $_POST['matrix'];
$gapCost = (empty($_POST['gapCost'])) ? '' : $_POST['gapCost'];
$filter = (empty($_POST['filter'])) ? 'F' : $_POST['filter'];
$softMask = (empty($_POST['softMask'])) ? 'F' : $_POST['softMask'];
$lowerCaseMask = (empty($_POST['lowerCaseMask'])) ? 'F' : $_POST['lowerCaseMask'];
$ungapAlign = (empty($_POST['ungapAlign'])) ? 'F' : $_POST['ungapAlign'];
$alignmentView = (empty($_POST['outFmt'])) ? 0 : $_POST['outFmt'];
$geneticCode = (empty($_POST['qCode'])) ? '' : $_POST['qCode'];
$dbGeneticCode = (empty($_POST['dbCode'])) ? '' : $_POST['dbCode'];
$otherParam = (empty($_POST['OTHER_ADVANCED'])) ? '' : $_POST['OTHER_ADVANCED'];
if ($otherParam) {
if (!preg_match("/^\s+$/", $otherParam) && !preg_match("/^\s*\-[A-Za-z]/", $otherParam)) {
echo "Error: The other advanced options must start with \"-\"";
exit;
}
}
$advanceParam = "$expect!#%$wordSize!#%$targetSeqs!#%$mmScore!#%$matrix!#%$gapCost!#%$filter!#%$softMask!#%$lowerCaseMask!#%$ungapAlign!#%$alignmentView!#%$geneticCode!#%$dbGeneticCode!#%$otherParam";
}else {
$advanceParam = "";
}
if (!$alignmentView) {
$alignmentView = 0;
}
if($blast_flag == 1) {
$nlstr = chr(10);
$crstr = chr(13);
if($_FILES['queryfile']['name']) {
$uploadfile = "$dataPath/$jobid.blastinput.txt";
if (move_uploaded_file($_FILES['queryfile']['tmp_name'], $uploadfile)) {
}else {
print "Couldn't upload the file. Here's some debugging info:\n";
print_r($_FILES);
exit;
}
@ $fp = fopen($uploadfile, "r");
if(!$fp) {
echo "<p><strong> Error: couldn't open $uploadfile </strong></p></body></html>";
exit;
}
$buffer = fread($fp, filesize($uploadfile));
fclose($fp);
if(!preg_match("/>/", $buffer)) {
echo "<p style='color: red'>Error: The uploading sequence file is not in fasta format. Please format your sequence file and upload again.</p><br>";
exit;
}else{
if(!preg_match("/$nlstr/", $buffer)) {
$buffer_mod = str_replace($crstr, $nlstr, $buffer);
$buffer = $buffer_mod;
}
$i = 0;
while(substr($buffer, $i, 1) != ">") {
$i++;
}
$buffer = substr($buffer, $i);
@ $fp = fopen($uploadfile, "w", 1);
if(!$fp) {
echo "<p><strong> Error: ouldn't open $uploadfile </strong></p></body></html>";
exit;
}
fwrite($fp, $buffer);
fclose($fp);
}
}elseif($querySeq && !preg_match("/^\s+$/", $querySeq)) {
@ $fp1=fopen("$dataPath/$jobid.blastinput.txt", "w",1);
if (!$fp1)
{
echo "<p><strong> Error: couldn't open $dataPath/$jobid.blastinput.txt </strong></p></body></html>";
exit;
}
fwrite($fp1, $querySeq);
fclose($fp1);
}else {
echo "<p style='color: red'>Error: please enter your query sequence or upload your fasta sequence file.</p><br>";
exit;
}
if(!$_FILES['blastagainstfile']['name'] && !$patientIDarray[0]) {
echo "<p style='color: red'>Error: please choose database(s) or upload your fasta sequence file to blast against.</p><br>";
exit;
}
if($_FILES['blastagainstfile']['name']) {
$uploadfile = "$dataPath/$jobid.blastagainst.txt";
if (move_uploaded_file($_FILES['blastagainstfile']['tmp_name'], $uploadfile)) {
}else {
print "Couldn't upload file. Here's some debugging info:\n";
print_r($_FILES);
exit;
}
@ $fp = fopen($uploadfile, "r");
if(!$fp) {
echo "<p><strong> Error: ouldn't open $uploadfile </strong></p></body></html>";
exit;
}
$buffer = fread($fp, filesize($uploadfile));
fclose($fp);
if(!preg_match("/>/", $buffer)) {
echo "<p style='color: red'>Error: The uploading sequence file to blast against is not in fasta format. Please format your sequence file and upload again.</p><br>";
exit;
}else{
if(!preg_match("/$nlstr/", $buffer)) {
$buffer_mod = str_replace($crstr, $nlstr, $buffer);
$buffer = $buffer_mod;
}
$i = 0;
while(substr($buffer, $i, 1) != ">") {
$i++;
}
$buffer = substr($buffer, $i);
@ $fp = fopen($uploadfile, "w", 1);
if(!$fp) {
echo "<p><strong> Error: couldn't open $uploadfile </strong></p></body></html>";
exit;
}
fwrite($fp, $buffer);
fclose($fp);
}
}
}
if($cutoffType == 'pct') {
$criterion = $pct_cutoff;
}
if($cutoffType == 'blst') {
$criterion = $blst_cutoff;
}
if(!$opt || $opt == 'wait') {
$progressdot = "image/progressdot.png";
echo "<p><strong>Your job is being processed ";
for($i = 0; $i <= ($dot%6); $i++) {
echo "<img src='$progressdot'>";
}
echo "</strong></p>";
$dot += 1;
echo "<p>Your job id is $jobid.</p>";
echo "<p>Please wait here to watch the progress of your job.</p>";
echo "<p>This page will update itself automatically until search is done.</p>";
}
if(!$opt || $opt == 'wait') {
echo "<META HTTP-EQUIV=\"refresh\"
content=\"10;URL=blastresult.php?jobid=$jobid&alignmentView=$alignmentView&opt=wait&dot=$dot\">";
echo "<META HTTP-EQUIV=\"expires\"
CONTENT=\"now\">";
}
if($blast_flag == 1) {
$blastagainst = "";
if ($program == "blastn" || $program == "tblastn" || $program == "tblastx") {
$dbPath = "./db/nucleotide";
}else {
$dbPath = "./db/protein";
}
if($blastagainstfile) {
$blastagainst = "$dataPath/$jobid.blastagainst.txt";
}
if ($patientIDarray) {
for ($i = 0; $i < sizeof($patientIDarray); $i++) {
$blastagainst .= " $dbPath/$patientIDarray[$i]";
}
}
$basicParam = "$jobid!#%$searchType!#%$blastagainst!#%$program!#%$blastpath";
/*create child process to run perl script which do the blast search and write output data to apropriate files*/
system('perl blast.pl '.escapeshellarg($basicParam).' '.escapeshellarg($advanceParam)." >/dev/null &");
}
/* error log if there is error in BLAST */
$errFile = "$dataPath/$jobid.err";
/* parent process continue here to check child process done or not */
$filename = "$dataPath/$jobid.blaststring.txt";
if (file_exists($errFile) && filesize($errFile) > 0) {
if(!$opt || $opt == 'wait') {
echo "<script LANGUAGE=JavaScript>";
echo "location.replace('blastresult.php?jobid=$jobid&opt=none')";
echo "</script>";
}else {
echo "<p>There is error in executing BLAST. Following is the error message:<p>";
$fperr = fopen("$dataPath/$jobid.err", "r");
if(!$fperr) {
echo "<p><strong> $jobid.err error: $errors </strong></p></body></html>";
exit;
}
while (!feof($fperr))
{
$line = rtrim(fgets($fperr));
echo "$line<br>";
}
fclose($fperr);
}
}elseif(file_exists($filename)) {
if ($alignmentView) {
echo "<script LANGUAGE=JavaScript>";
echo "location.replace('data/$jobid.blast')";
echo "</script>";
}else {
if($blast_flag == 'Parse again') {
$print_flag = 0;
$cutoff_count = 0;
@ $fpout=fopen("$dataPath/$jobid.par", "r");
if (!$fpout)
{
echo "<p><strong> $jobid.par error: $phperrormsg </strong></p></body></html>";
exit;
}
@ $fpout3 = fopen("$dataPath/$jobid.out.par", "w", 1);
if(!$fpout3) {
echo "<p><strong> $jobid.out.par error: $errors </strong></p></body></html>";
exit;
}
while (!feof($fpout))
{
$fpout2_str = '';
$line = rtrim(fgets($fpout));
if (!$line) {
continue;
}
list($page, $query_name, $match_name, $score, $identities, $percentage, $e_value, $link) = preg_split("/\t/", $line);
if($cutoffType == 'pct') {
$subject = $percentage;
}else {
$subject = $score;
}
if($subject >= $criterion) {
fwrite($fpout3, "$page\t$query_name\t$match_name\t$score\t$identities\t$percentage\t$e_value\t$link\n");
$cutoff_count++;
}
}
fclose ($fpout);
fclose($fpout3);
@ $fp = fopen("$dataPath/$jobid.blastcount.txt", "w", 1);
if(!$fp) {
echo "<p><strong> error: $php_errormsg </strong></p></body></html>";
exit;
}else {
fwrite($fp, "$cutoff_count\n");
}
fclose($fp);
}
$filename = "$dataPath/$jobid.blastcount.txt";
while(!file_exists($filename)) {}
if(!$opt || $opt == 'wait') {
echo "<script LANGUAGE=JavaScript>";
echo "location.replace('blastresult.php?jobid=$jobid&opt=none')";
echo "</script>";
}else {
@ $fp = fopen("$dataPath/$jobid.blastcount.txt", "r");
if(!$fp) {
echo "<p><strong> error: $php_errormsg </strong></p></body></html>";
exit;
}
if(!feof($fp)) {
$cutoff_count = fgets($fp);
}
fclose($fp);
@ $fp = fopen("$dataPath/$jobid.blaststring.txt", "r");
if(!$fp) {
echo "<p><strong> error: $php_errormsg </strong></p></body></html>";
exit;
}
if(!feof($fp)) {
$blastagainststring = rtrim(fgets($fp));
}
fclose($fp);
if($cutoff_count == 0) {
echo "<p>No comparison meets cutoff criterion. Please change expect value to blast again.</p>";
}else {
echo "<p><a href=data/$jobid.blast1.html target='_blank'>Inspect BLAST output</a><br>";
echo "<form action='blastresult.php?jobid=$jobid&opt=$opt' method='post'>";
echo "<p>Filter current page by score:</p>";
echo "<p> Show <select name='filt_val'>";
echo "<option value='0' selected>- All -";
echo "<option value='1'>Top score";
echo "<option value='5'>Top 5 scores";
echo "<option value='10'>Top 10 scores";
echo "</select> for each query sequence <input type='submit' name='filter_flag' value='Filter'></font></p>";
echo "<p>Re-parse current blast results (please select cutoff criterion):</p>";
echo "<p><table style='font-size: 12px'>";
echo "<tr><td><input type='radio' checked name='cutoffType' value='pct'>Similarity percentage</td><td></td>";
echo "<td>Cutoff %: </td><td><input type='text' name='pct_cutoff' value=95 size=6 maxlength=6></td></tr>";
echo "<tr><td><input type='radio' name='cutoffType' value='blst'>Blast score</td><td></td>";
echo "<td>Cutoff score: </td><td><input type='text' name='blst_cutoff' value=1000 size=6 maxlength=6></td>";
echo "<td><input type='submit' name='blast_flag' value='Parse again'>";
echo "</td></tr></table></p>";
echo "</form>";
echo "<form action='sequence.php?jobid=$jobid' method='post' target='_blank' onsubmit=\"return checkform(this);\">";
echo "<p>Retrieve and download subject sequences in FASTA format: ";
echo "<input type='radio' checked name='seqtype' value='entire'>Entire sequence ";
echo "<input type='radio' name='seqtype' value='mapping'>Region mapped to query</p>";
echo "<p><input type='checkbox' name='dldseq' value='all'> Check here to download All sequences... ";
echo "OR select particular sequences of interest below</p>";
echo "<p><input type='submit' value='Submit'> your selection of sequences to download</p>";
echo "<p><table border = 1 style='font-size:10px' width=100% class='sortable'>";
echo "<thead><tr align='center'><th>Query</th><th>Subject</th><th>Score</th><th>Identities (Query length)</th><th>Percentage</th><th>Expect</th></tr></thead>";
echo "<tbody>";
@ $fp = fopen("$dataPath/$jobid.download.txt", "w", 1) or die("Cannot open file: $jobid.download.txt");
if($blast_flag == 'Parse again' || ($opt == 'none' && !$filter_flag)) {
@ $fpout3=fopen("$dataPath/$jobid.out.par", "r");
if(!$fpout3) {
echo "<p><strong> error: $php_errormsg </strong></p></body></html>";
exit;
}
$i = 0;
$queryName = $preQueryName = "";
while(!feof($fpout3)) {
$row = fgets($fpout3);
if (!$row) {
continue;
}
$element = preg_split("/\t/", $row);
$page = $element[0];
$queryName = $element[1];
$target_name = $element[7];
$var_target = $page."\t".$element[1]."\t".$element[2];
if(count($element) != 1) {
if($queryName == $preQueryName) {
$i++;
}else {
$i = 0;
}
if($i < 10) {
echo "<tr align='center'><td>$element[1]</td><td align=left><input type='checkbox' id='checkedSeq' name='target[]' value=\"$var_target\">$target_name</td><td><a href=data/$jobid.blast$page.html#$element[1]$element[2] target='_blank'>$element[3]</a></td><td>$element[4]</td><td>$element[5]</td><td>$element[6]</td></tr>";
fwrite($fp, "$var_target\n");
}
}
$preQueryName = $queryName;
}
fclose($fpout3);
}
if($filter_flag == 'Filter')
{
@ $fpout3=fopen("$dataPath/$jobid.out.par", "r");
if(!$fpout3) {
echo "<p><strong> error: $php_errormsg </strong></p></body></html>";
exit;
}
$i = 0;
while(!feof($fpout3)) {
$row = fgets($fpout3);
if (!$row) {
continue;
}
$element = preg_split("/\t/", $row);
$page = $element[0];
$target_name = $element[7];
$var_target = $page."\t".$element[1]."\t".$element[2];
if(count($element) != 1) {
if($filt_val != 0) {
if($i == 0) {
$query_name = $element[1];
echo "<tr align='center'><td>$element[1]</td><td align=left><input type='checkbox' id='checkedSeq' name='target[]' value=\"$var_target\">$target_name</td><td><a href=data/$jobid.blast$page.html#$element[1]$element[2] target='_blank'>$element[3]</a></td><td>$element[4]</td><td>$element[5]</td><td>$element[6]</td></tr>";
fwrite($fp, "$var_target\n");
$i++;
}elseif($query_name == $element[1] && $i < $filt_val) {
echo "<tr align='center'><td>$element[1]</td><td align=left><input type='checkbox' id='checkedSeq' name='target[]' value=\"$var_target\">$target_name</td><td><a href=data/$jobid.blast$page.html#$element[1]$element[2] target='_blank'>$element[3]</a></td><td>$element[4]</td><td>$element[5]</td><td>$element[6]</td></tr>";
fwrite($fp, "$var_target\n");
$i++;
}elseif($query_name != $element[1]) {
echo "<tr align='center'><td>$element[1]</td><td align=left><input type='checkbox' id='checkedSeq' name='target[]' value=\"$var_target\">$target_name</td><td><a href=data/$jobid.blast$page.html#$element[1]$element[2] target='_blank'>$element[3]</a></td><td>$element[4]</td><td>$element[5]</td><td>$element[6]</td></tr>";
$query_name = $element[1];
fwrite($fp, "$var_target\n");
$i=1;
}
}else {
echo "<tr align='center'><td>$element[1]</td><td align=left><input type='checkbox' id='checkedSeq' name='target[]' value=\"$var_target\">$target_name</td><td><a href=data/$jobid.blast$page.html#$element[1]$element[2] target='_blank'>$element[3]</a></td><td>$element[4]</td><td>$element[5]</td><td>$element[6]</td></tr>";
fwrite($fp, "$var_target\n");
}
}
}
fclose($fpout3);
}
fclose($fp);
echo "</tbody></table></form>";
echo "<p><a href=\"#top\">Top</a>";
}
}
}
}
?>
</div>
<div id="footer" align="center">
<p><font color='gray'>© 2005-2010 University of Washington. All rights reserved. <a href=docs/termsofservice.html>Terms of Service</a></p>
</div>
</body>
</html>