Download: HTML, Tab-Delimited, XML
The following table summarizes the results of your BLAST. To see additional information about each hit including the alignment, click on that row in the table to expand it.
array('data' => '#', 'class' => array('number')), 'query' => array('data' => 'Query Name', 'class' => array('query')), 'hit' => array('data' => 'Hit Name', 'class' => array('hit')), 'evalue' => array('data' => 'E-Value', 'class' => array('evalue')), 'arrow-col' => array('data' => '', 'class' => array('arrow-col')) ); $rows = array(); $count = 0; // Parse the BLAST XML to generate the rows of the table // where each hit results in two rows in the table: 1) A summary of the query/hit and // significance and 2) additional information including the alignment foreach($xml->{'BlastOutput_iterations'}->children() as $iteration) { $children_count = $iteration->{'Iteration_hits'}->children()->count(); if($children_count != 0) { foreach($iteration->{'Iteration_hits'}->children() as $hit) { if (is_object($hit)) { $count +=1; $zebra_class = ($count % 2 == 0) ? 'even' : 'odd'; $no_hits = FALSE; // SUMMARY ROW // If the id is of the form gnl|BL_ORD_ID|### then the parseids flag // to makeblastdb did a really poor job. In thhis case we want to use // the def to provide the original FASTA header. $hit_name = (preg_match('/BL_ORD_ID/', $hit->{'Hit_id'})) ? $hit->{'Hit_def'} : $hit->{'Hit_id'}; // If our BLAST DB is configured to handle link-outs then use the // regex & URL prefix provided to create one. if ($linkout) { if (preg_match($linkout_regex, $hit_name, $linkout_match)) { $hit_name = l( $linkout_match[1], $linkout_urlprefix . $linkout_match[1], array('attributes' => array('target' => '_blank')) ); } } $score = $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_score'}; $evalue = $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_evalue'}; $query_name = $iteration->{'Iteration_query-def'}; $row = array( 'data' => array( 'number' => array('data' => $count, 'class' => array('number')), 'query' => array('data' => $query_name, 'class' => array('query')), 'hit' => array('data' => $hit_name, 'class' => array('hit')), 'evalue' => array('data' => $evalue, 'class' => array('evalue')), 'arrow-col' => array('data' => '', 'class' => array('arrow-col')) ), 'class' => array('result-summary') ); $rows[] = $row; // ALIGNMENT ROW (collapsed by default) // Process HSPs $HSPs = array(); foreach ($hit->{'Hit_hsps'}->children() as $hsp_xml) { $HSPs[] = (array) $hsp_xml; } $row = array( 'data' => array( 'number' => '', 'query' => array( 'data' => theme('blast_report_alignment_row', array('HSPs' => $HSPs)), 'colspan' => 4, ) ), 'class' => array('alignment-row', $zebra_class), 'no_striping' => TRUE ); $rows[] = $row; }// end of if - checks $hit } //end of foreach - iteration_hits } // end of if - check for iteration_hits else { // Currently where the "no results" is added. $query_name = $iteration->{'Iteration_query-def'}; $query_with_no_hits[] = $query_name; } // end of else } if ($no_hits) { print ''; } else { // We want to warn the user if some of their query sequences had no hits. if (!empty($query_with_no_hits)) { print ''; } // Actually print the table. if (!empty($rows)) { print theme('table', array( 'header' => $header, 'rows' => $rows, 'attributes' => array('id' => 'blast_report'), )); } } } else { drupal_set_title('BLAST: Error Encountered'); print 'We encountered an error and are unable to load your BLAST results.
'; } ?>