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- <?php
- /**
- * Display the results of a BLAST job execution
- */
- // Set ourselves up to do link-out if our blast database is configured to do so.
- $linkout = FALSE;
- if ($blast_job->blastdb->linkout->none === FALSE) {
- $linkout_type = $blast_job->blastdb->linkout->type;
- $linkout_regex = $blast_job->blastdb->linkout->regex;
- // Note that URL prefix is not required if linkout type is 'custom'
- if (isset($blast_job->blastdb->linkout->db_id->urlprefix) && !empty($blast_job->blastdb->linkout->db_id->urlprefix)) {
- $linkout_urlprefix = $blast_job->blastdb->linkout->db_id->urlprefix;
- }
- // Check that we can determine the linkout URL.
- // (ie: that the function specified to do so, exists).
- if (function_exists($blast_job->blastdb->linkout->url_function)) {
- $url_function = $blast_job->blastdb->linkout->url_function;
- $linkout = TRUE;
- }
- }
- // Handle no hits. This following array will hold the names of all query
- // sequences which didn't have any hits.
- $query_with_no_hits = array();
- // Furthermore, if no query sequences have hits we don't want to bother listing
- // them all but just want to give a single, all-include "No Results" message.
- $no_hits = TRUE;
- ?>
- <script type="text/javascript">
- // JQuery controlling display of the alignment information (hidden by default)
- $(document).ready(function(){
- // Hide the alignment rows in the table
- // (ie: all rows not labelled with the class "result-summary" which contains the tabular
- // summary of the hit)
- $("#blast_report tr:not(.result-summary)").hide();
- $("#blast_report tr:first-child").show();
- // When a results summary row is clicked then show the next row in the table
- // which should be corresponding the alignment information
- $("#blast_report tr.result-summary").click(function(){
- $(this).next("tr").toggle();
- $(this).find(".arrow").toggleClass("up");
- });
- });
- </script>
- <style>
- .no-hits-message {
- color: red;
- font-style: italic;
- }
- </style>
- <div class="blast-report">
- <!-- Provide Information to the user about their blast job -->
- <div class="blast-job-info">
- <div class="blast-download-info"><strong>Download</strong>:
- <a href="<?php print '../../' . $blast_job->files->result->html; ?>">Alignment</a>,
- <a href="<?php print '../../' . $blast_job->files->result->tsv; ?>">Tab-Delimited</a>,
- <a href="<?php print '../../' . $blast_job->files->result->xml; ?>">XML</a>,
- <a href="<?php print '../../' . $blast_job->files->result->gff; ?>">GFF3</a>
- </div>
- <br />
- <div class="blast-query-info"><strong>Query Information</strong>:
- <?php print $blast_job->files->query;?></div>
- <div class="blast-target-info"><strong>Search Target</strong>:
- <?php print $blast_job->blastdb->db_name;?></div>
- <div class="blast-date-info"><strong>Submission Date</strong>:
- <?php print format_date($blast_job->date_submitted, 'medium');?></div>
- <div class="blast-cmd-info"><strong>BLAST Command executed</strong>:
- <?php print $blast_job->blast_cmd;?></div>
- <br />
- <div class="num-results">
- <strong>Number of Results</strong>: <?php print $num_results; ?>
- </div>
- </div>
- <?php
- if ($show_cvit_diagram) {
- ?>
- <!-- CViTjs image of BLAST hits, if enabled -->
- <div class="cvitjs">
- <div id="title-div"><h2>Whole Genome Visualization of BLAST hits</h2></div>
- <div id="cvit-div"></div>
- </div>
- <?php
- }
- ?>
- <br />
- <div class="report-table">
- <?php
- /**
- * We are using the drupal table theme functionality to create this listing
- * @see theme_table() for additional documentation
- */
- if ($xml) {
- ?>
- <h2>Resulting BLAST hits</h2>
- <p>The following table summarizes the results of your BLAST.
- Click on a <em>triangle </em> on the left to see the alignment and a visualization of the hit,
- and click the <em>target name </em> to get more information about the target hit.</p>
- <?php
- // Specify the header of the table
- $header = array(
- 'arrow-col' => array('data' => '', 'class' => array('arrow-col')),
- 'number' => array('data' => '#', 'class' => array('number')),
- 'query' => array('data' => 'Query Name (Click for alignment & visualization)', 'class' => array('query')),
- 'hit' => array('data' => 'Target Name', 'class' => array('hit')),
- 'evalue' => array('data' => 'E-Value', 'class' => array('evalue')),
- );
- $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();
- // Save some information needed for the hit visualization.
- $target_name = '';
- $q_name = $iteration->{'Iteration_query-def'};
- $query_size = $iteration->{'Iteration_query-len'};
- $target_size = $iteration->{'Iteration_stat'}->{'Statistics'}->{'Statistics_db-len'};
- if ($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
- // -- Save additional information needed for the summary.
- $score = (float) $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_score'};
- $evalue = (float) $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_evalue'};
- $query_name = (string) $iteration->{'Iteration_query-def'};
- // 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'};
- // Used for the hit visualization to ensure the name isn't truncated.
- $hit_name_short = (preg_match('/^([^\s]+)/', $hit_name, $matches)) ? $matches[1] : $hit_name;
- // Round e-value to two decimal values.
- $rounded_evalue = '';
- if (strpos($evalue,'e') != false) {
- $evalue_split = explode('e', $evalue);
- $rounded_evalue = round($evalue_split[0], 2, PHP_ROUND_HALF_EVEN);
- $rounded_evalue .= 'e' . $evalue_split[1];
- }
- else {
- $rounded_evalue = $evalue;
- }
- // State what should be in the summary row for theme_table() later.
- $summary_row = array(
- 'data' => array(
- 'arrow-col' => array('data' => '<div class="arrow"></div>', 'class' => array('arrow-col')),
- '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' => $rounded_evalue, 'class' => array('evalue')),
- ),
- 'class' => array('result-summary')
- );
- // ALIGNMENT ROW (collapsed by default)
- // Process HSPs
- $HSPs = array();
- // We need to save some additional summary information in order to draw the
- // hit visualization. First, initialize some variables...
- $track_start = INF;
- $track_end = -1;
- $hsps_range = '';
- $hit_hsps = '';
- $hit_hsp_score = '';
- $target_size = $hit->{'Hit_len'};
- $Hsp_bit_score = '';
- // Then for each hit hsp, keep track of the start of first hsp and the end of
- // the last hsp. Keep in mind that hsps might not be recorded in order.
- foreach ($hit->{'Hit_hsps'}->children() as $hsp_xml) {
- $HSPs[] = (array) $hsp_xml;
- if ($track_start > $hsp_xml->{'Hsp_hit-from'}) {
- $track_start = $hsp_xml->{'Hsp_hit-from'} . "";
- }
- if ($track_end < $hsp_xml->{'Hsp_hit-to'}) {
- $track_end = $hsp_xml->{'Hsp_hit-to'} . "";
- }
- // The BLAST visualization code requires the hsps to be formatted in a
- // very specific manner. Here we build up the strings to be submitted.
- // hits=4263001_4262263_1_742;4260037_4259524_895_1411;&scores=722;473;
- $hit_hsps .= $hsp_xml->{'Hsp_hit-from'} . '_' .
- $hsp_xml->{'Hsp_hit-to'} . '_' .
- $hsp_xml->{'Hsp_query-from'} . '_' . $hsp_xml->{'Hsp_query-to'} .
- ';';
- $Hsp_bit_score .= $hsp_xml->{'Hsp_bit-score'} .';';
- }
- // Finally record the range.
- // @todo figure out why we arbitrarily subtract 50,000 here...
- // @more removing the 50,000 and using track start/end appears to cause no change...
- $range_start = (int) $track_start;// - 50000;
- $range_end = (int) $track_end;// + 50000;
- if ($range_start < 1) $range_start = 1;
- // Call the function to generate the hit image.
- $hit_img = generate_blast_hit_image($target_name, $Hsp_bit_score, $hit_hsps,
- $target_size, $query_size, $q_name, $hit_name_short);
- // get blast program
- $blast_cmd_arr = explode(' ',trim($blast_job->blast_cmd));
- $blast_cmd_program = $blast_cmd_arr[0];
- // State what should be in the alignment row for theme_table() later.
- $alignment_row = array(
- 'data' => array(
- 'arrow' => array(
- 'data' => theme('blast_report_alignment_row', array('HSPs' => $HSPs, 'hit_visualization' => $hit_img, 'blast_program' => $blast_cmd_program)),
- 'colspan' => 5,
- ),
- ),
- 'class' => array('alignment-row', $zebra_class),
- 'no_striping' => TRUE
- );
- // LINK-OUTS.
- // It was determined above whether link-outs were supported for the
- // tripal blast database used as a search target. Thus we only want to
- // determine a link-out if it's actually supported... ;-)
- if ($linkout) {
- // First extract the linkout text using the regex provided through
- // the Tripal blast database node.
- if (preg_match($linkout_regex, $hit_name, $linkout_match)) {
- $hit->{'linkout_id'} = $linkout_match[1];
- $hit->{'hit_name'} = $hit_name;
- // Allow custom functions to determine the URL to support more complicated
- // link-outs rather than just using the tripal database prefix.
- $hit_name = call_user_func(
- $url_function,
- $linkout_urlprefix,
- $hit,
- array(
- 'query_name' => $query_name,
- 'score' => $score,
- 'e-value' => $evalue,
- 'HSPs' => $HSPs,
- 'Target' => $blast_job->blastdb->db_name,
- 'RegEx' => $linkout_regex,
- )
- );
- }
- // Replace the target name with the link.
- $summary_row['data']['hit']['data'] = $hit_name;
- }
- // ADD TO TABLE ROWS
- $rows[] = $summary_row;
- $rows[] = $alignment_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[] = $query_name;
- }//no results
- }//end of foreach - BlastOutput_iterations
- if ($no_hits) {
- print '<p class="no-hits-message">No results found.</p>';
- }
- else {
- // We want to warn the user if some of their query sequences had no hits.
- if (!empty($query_with_no_hits)) {
- print '<p class="no-hits-message">Some of your query sequences did not '
- . 'match to the database/template. They are: '
- . implode(', ', $query_with_no_hits) . '.</p>';
- }
- // Actually print the table.
- if (!empty($rows)) {
- print theme('table', array(
- 'header' => $header,
- 'rows' => $rows,
- 'attributes' => array('id' => 'blast_report'),
- 'sticky' => FALSE
- ));
- }
- }//handle no hits
- }//XML exists
- elseif ($too_many_results) {
- print '<div class="messages error">Your BLAST resulted in '. number_format(floatval($num_results)) .' results which is too many to reasonably display. We have provided the result files for Download at the top of this page; however, we suggest you re-submit your query using a more stringent e-value (i.e. a smaller number).</div>';
- }
- else {
- drupal_set_title('BLAST: Error Encountered');
- print '<div class="messages error">We encountered an error and are unable to load your BLAST results.</div>';
- }
- ?>
- <p><?php print l(
- 'Edit this query and re-submit',
- $blast_form_url,
- array('query' => array('resubmit' => blast_ui_make_secret($job_id))));
- ?></p>
- </div>
- <?php print theme('blast_recent_jobs', array()); ?>
- </div>
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