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 (Click for alignment & visualization)', '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(); //@deepaksomanadh: Code added for BLAST visualization // parameters that need to be passed for BLAST image generation $target_name = ''; $q_name = $xml->{'BlastOutput_query-def'}; $query_size = $xml->{'BlastOutput_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; // RETRIEVE INFO $hit_name = (preg_match('/BL_ORD_ID/', $hit->{'Hit_id'})) ? $hit->{'Hit_def'} : $hit->{'Hit_id'}; $score = $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_score'}; $evalue = $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_evalue'}; $query_name = $iteration->{'Iteration_query-def'}; // Round e-val 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; } // ALIGNMENT ROW (collapsed by default) // Process HSPs // @deepaksomanadh: Code added for BLAST visualization // hit array and corresponding bit scores // hits=4263001_4262263_1_742;4260037_4259524_895_1411;&scores=722;473; $HSPs = array(); $hit_hsps = ''; $hit_hsp_score = ''; foreach ($hit->{'Hit_hsps'}->children() as $hsp_xml) { $HSPs[] = (array) $hsp_xml; $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 .= $hsp_xml->{'Hsp_bit-score'} .';'; } // SUMMARY ROW // If the id is of the form gnl|BL_ORD_ID|### then the parseids flag // to makeblastdb did a really poor job. In this case we want to use // the def to provide the original FASTA header. // If our BLAST DB is configured to handle link-outs then use the // regex & URL prefix provided to create one. if ($linkout) { if (preg_match($linkout_regex, $hit_name, $linkout_match)) { $linkout_id = $linkout_match[1]; $hit->{'linkout_id'} = $linkout_id; $hit->{'hit_name'} = $hit_name; $hit_url = call_user_func( $url_function, $linkout_urlprefix, $hit, array( 'query_name' => $query_name, 'score' => $score, 'e-value' => $evalue, 'HSPs' => $HSPs ) ); if ($hit_url) { $hit_name = l( $linkout_id, $hit_url, array('attributes' => array('target' => '_blank')) ); } } } //@deepaksomanadh: Code added for BLAST visualization // get the image and display $hit_img = generateImage($target_name, $Hsp_bit_score, $hit_hsps, $target_size, $query_size, $q_name); ob_start(); // Start buffering the output imagepng($hit_img, null, 0, PNG_NO_FILTER); $b64 = base64_encode(ob_get_contents()); // Get what we've just outputted and base64 it imagedestroy($hit_img); ob_end_clean(); // Print the HTML tag with the image embedded $hit_img = '
';
$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' => $rounded_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
$row = array(
'data' => array(
'number' => '',
'query' => array(
'data' => theme('blast_report_alignment_row', array('HSPs' => $HSPs)),
),
'hit' => array(
'data' => $hit_img,
'colspan' => 3,
),
),
'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.
'; } ?>