Resulting BLAST hits

The following table summarizes the results of your BLAST. Click on a triangle on the left to see the alignment and a visualization of the hit, and click the target name to get more information about the target hit.

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' => '', '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 '

No results found.

'; } else { // We want to warn the user if some of their query sequences had no hits. if (!empty($query_with_no_hits)) { print '

Some of your query sequences did not ' . 'match to the database/template. They are: ' . implode(', ', $query_with_no_hits) . '.

'; } // 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 ''; } else { drupal_set_title('BLAST: Error Encountered'); print ''; } ?>

array('resubmit' => blast_ui_make_secret($job_id)))); ?>