Source code of BlastXML.php class
<?php
/**
* @file BlastXML.php
* Provides a class for handling Blast XML files.
* Orginally writen by Riadh Hammami
*/
class BlastXML
{
private $data;
private $params = array();
private $Iterations = array();
public function __construct(SimpleXMLElement $BlastXMLData = NULL)
{
if ($BlastXMLData) {
$this--->setData($BlastXMLData);
}
}
public function setData(SimpleXMLElement $BlastXMLData)
{
$this->data = $BlastXMLData->data;
$this->parameters();
//$BlastXMLData->asXML();
$this->SetIterations();
return $this;
}
private function SetIterations()
{
$iterations = $this->data->xpath('//Iteration');
if (isset($iterations)) {
foreach ($iterations as $iteration) {
$this->Iterations[] = $this->fetch_iteration($iteration);
}
}
}
private function fetch_iteration(SimpleXMLElement $iteration)
{
$id = $iteration->{"Iteration_query-ID"};
$query = $iteration->{"Iteration_query-def"};
$length = $iteration->{"Iteration_query-len"};
$hits = $iteration->xpath('.//Iteration_hits/Hit');
$Hits_array = array();
foreach ($hits as $hit) {
$Hit_id = $hit->{"Hit_id"};
$Hit_def = $hit->{"Hit_def"};
$Hit_accession = $hit->{"Hit_accession"};
$Hit_len = $hit->{"Hit_len"};
$Hsps = $hit->xpath('.//Hsp');
$Hsp_array = array();
foreach ($Hsps as $Hsp) {
$Hsp_num = $Hsp->{"Hsp_num"};
$Hsp_bit_score = $Hsp->{"Hsp_bit-score"};
$Hsp_score = $Hsp->{"Hsp_score"};
$Hsp_evalue = $Hsp->{"Hsp_evalue"};
$Hsp_query_from = $Hsp->{"Hsp_query-from"};
$Hsp_query_to = $Hsp->{"Hsp_query-to"};
$Hsp_hit_from = $Hsp->{"Hsp_hit-from"};
$Hsp_hit_to = $Hsp->{"Hsp_hit-to"};
$Hsp_query_frame = $Hsp->{"Hsp_query-frame"};
$Hsp_hit_frame = $Hsp->{"Hsp_hit-frame"};
$Hsp_identity = $Hsp->{"Hsp_identity"};
$Hsp_positive = $Hsp->{"Hsp_positive"};
$Hsp_gaps = $Hsp->{"Hsp_gaps"};
$Hsp_align_len = $Hsp->{"Hsp_align-len"};
$Hsp_qseq = $Hsp->{"Hsp_qseq"};
$Hsp_hseq = $Hsp->{"Hsp_hseq"};
$Hsp_midline = $Hsp->{"Hsp_midline"};
$Hsp_array[] = array("Hsp_num" => (int)$Hsp_num[0],
"Hsp_bit-score" => (float)$Hsp_bit_score[0],
"Hsp_score" => (float)$Hsp_score[0],
"Hsp_evalue" => (float)$Hsp_evalue[0],
"Hsp_query-from" => (int)$Hsp_query_from[0],
"Hsp_query-to" => (int)$Hsp_query_to[0],
"Hsp_hit-from" => (int)$Hsp_hit_from[0],
"Hsp_hit-to" => (int)$Hsp_hit_to[0],
"Hsp_query-frame"=> (int)$Hsp_query_frame[0],
"Hsp_hit-frame" => (int)$Hsp_hit_frame[0],
"Hsp_identity" => (int)$Hsp_identity[0],
"Hsp_positive" => (int)$Hsp_positive[0],
"Hsp_gaps" => (int)$Hsp_gaps[0],
"Hsp_align-len" => (int)$Hsp_align_len[0],
"Hsp_qseq" => (string)$Hsp_qseq[0],
"Hsp_hseq" => (string)$Hsp_hseq[0],
"Hsp_midline" => (string)$Hsp_midline[0]);
}
$Hits_array[] = array ("Hit_id"=> (string)$Hit_id[0],
"Hit_def"=> (string)$Hit_def[0],
"Hit_accession"=> (string)$Hit_accession[0],
"Hit_len"=> (int)$Hit_len[0],
"Hit_hsps"=> $Hsp_array);
}
$stats = $iteration->xpath('.//Iteration_stat/Statistics');
$Statistics_db_num = $stats->{"Statistics_db-num"};
$Statistics_db_len = $stats->{"Statistics_db-len"};
$Statistics_hsp_len = $stats->{"Statistics_hsp-len"};
$Statistics_eff_space = $stats->{"Statistics_eff-space"};
$Statistics_kappa = $stats->{"Statistics_kappa"};
$Statistics_lambda = $stats->{"Statistics_lambda"};
$Statistics_entropy = $stats->{"Statistics_entropy"};
$stats_array = array ("Statistics_db-num" => (int)$Statistics_db_num[0],
"Statistics_db-len" => (int)$Statistics_db_len[0],
"Statistics_hsp-len" => (int)$Statistics_hsp_len[0],
"Statistics_eff-space" => (float)$Statistics_eff_space[0],
"Statistics_kappa" => (float)$Statistics_kappa[0],
"Statistics_lambda" => (float)$Statistics_lambda[0],
"Statistics_entropy" => (float)$Statistics_entropy[0]);
$It_message = $iteration->{"Iteration_message"};
$iteration_message = NULL;
if (isset($It_message)) $iteration_message=(string)$It_message[0];
return array( "ID" => (string)$id[0],
"query" => (string)$query[0],
"length" => (int)$length[0],
"Hits" => $Hits_array,
"Statistics" => $stats_array,
"Iteration_message" => $iteration_message);
//return NULL;
}
private function parameters() {
$program = $this->data->xpath('//BlastOutput_program');
$version = $this->data->xpath('//BlastOutput_version');
$reference = $this->data->xpath('//BlastOutput_reference');
$db = $this->data->xpath('//BlastOutput_db');
$matrix = $this->data->xpath('//Parameters_matrix');
$expect = $this->data->xpath('//Parameters_expect');
$gap_open = $this->data->xpath('//Parameters_gap-open');
$gap_extend = $this->data->xpath('//Parameters_gap-extend');
$filter = $this->data->xpath('//Parameters_filter');
$this->params = array("program" => (string)$program[0],
"version" => (string)$version[0],
"reference" => (string)$reference[0],
"db" => (string)$db[0],
"matrix" => (string)$matrix[0],
"expect" => (int)$expect[0],
"gap-open" => (int)$gap_open[0],
"gap-extend" => (int)$gap_extend[0],
"filter" => (string)$filter[0]);
return $this->params;
}
public function program() { return $this->params["program"];}
public function version() { return $this->params["version"];}
public function reference() { return $this->params["reference"];}
public function db() { return $this->params["db"];}
public function matrix() { return $this->params["matrix"];}
public function Results() {return $this->Iterations;}
}
?>
Demo
<?php
include("BlastXML.php");
$filename="results.xml"; //XML Blast output file
$xml = simplexml_load_file($filename);
$blast = new BlastXML($xml);
//echo "Program :" . $blast->program() . "<br>";
echo "Version:" . $blast->version() . "<br>";
//echo "Reference:" . $blast->reference() . "<br>";
//echo "DB:" . $blast->db() . "<br>";
//echo "Matrix:" . $blast->matrix() . "<br>";
$Results = $blast->Results();
foreach($Results as $Result){
//var_dump($Results); // for debug purpose
echo "<b>Query= " . $Result["query"]. "</b><br>";
echo "<i>Length= " . $Result["length"]. "</i><br>";
if (count($Result["Hits"])>0) {
echo '<table width="700">';
echo "<tr><td align=\"center\"><b><br>Sequences</td><td><b><br>producing significant alignments:</td><td align=\"center\"><b>Score<br>(bits)</td><td align=\"center\"><b>E<br>Value</b></td></tr>";
foreach ($Result["Hits"] as $hit)
{
$id = $hit["Hit_id"];
$Name = $hit["Hit_def"];
$Score = $hit["Hit_hsps"][0]["Hsp_bit-score"];
$Evalue = $hit["Hit_hsps"][0]["Hsp_evalue"];
echo "<td align=\"center\"><div id='".$id."Table'>" ."<a href='" . $id . "'>" .$id . "</a></div></td>"
."<td><a href=\"" . $id . "\">" .$Name . "</a>" ."</td>"
."<td align=\"center\">" . $Score ."</td>"
."<td>".$Evalue ."</td>"
."</tr>";
}
echo "</table>";
} else {
echo $Result["Iteration_message"];
}
}
?>
