Tripal GBrowse: Added ability to align features from on library/analysis to another, generate a gff3 and load it into a gbrowse instance

tripal_gbrowse/tripal_gbrowse.align_features.inc

@@ -0,0 +1,647 @@
+<?php
+
+/**
+ * Form to initialize an align library tripal job
+ */
+function tripal_gbrowse_align_features_form ($form_state) {
+  $form = array();
+  
+  // compile all analysis' as options
+  $analysis_options = array();
+  $results = tripal_core_chado_select('analysis',array('analysis_id','name', 'program'), array());
+  foreach ($results as $r) {
+    $analysis_options[ 'A'.$r->analysis_id ] = $r->name .' --'.$r->program;
+  }
+  
+  // compile all libraries as options
+  $library_options = array();
+  $results = tripal_core_chado_select('library',array('library_id','name', 'uniquename'), array());
+  foreach ($results as $r) {
+    $library_options[ 'L'.$r->library_id ] = $r->name .' --'.$r->uniquename;
+  }  
+  
+  $form['description'] = array(
+    '#type' => 'item',
+    '#value' => 'This form allows you to select a query library/analysis and align the '
+      .'features that are part of that query library/analysis against those from a database '
+      .'library/analysis using BLAST. Depending upon the Alignment Criteria, the top BLAST '
+      .'result(s) for each query feature will be used to determine the location of the query '
+      .'feature on a database feature.',
+  );
+  
+  $form['q'] = array(
+    '#type' => 'fieldset',
+    '#title' => 'Features to be Aligned (Query)',
+    '#description' => 'Please select the library or analysis below which groups the features you '
+      .'want aligned together.',
+  );
+  
+  $form['q']['query'] = array(
+    '#type' => 'select',
+    '#title' => 'Query Features',
+    '#options' => array(
+      'Libraries' => $library_options,
+      "Analaysis'" => $analysis_options
+    ),
+    '#default_value' => $form_state['values']['query'],
+  );
+  
+  $form['d'] = array(
+    '#type' => 'fieldset',
+    '#title' => 'Features to Align To (Database)',
+    '#description' => 'Please select the library of analysis below, which contains the features '
+      .'you want to align the query features selected above to. Only features in the selected '
+      .'library/analysis with sequence data will be used.',
+  );
+
+  $form['d']['database'] = array(
+    '#type' => 'select',
+    '#title' => 'Database Features',
+    '#options' => array(
+      'Libraries' => $library_options,
+      "Analaysis'" => $analysis_options
+    ),
+    '#default_value' => $form_state['values']['database'],
+  );
+  
+  $form['b'] = array(
+    '#type' => 'fieldset',
+    '#title' => 'Alignment Criteria',
+  );
+  
+  $form['b']['program'] = array(
+  	'#type' => 'radios',
+  	'#title' => 'Alignment Program',
+  	'#options' => array(
+  		'blast' => 'BLAST',
+  		'blat' => 'BLAT',
+  	),
+  	'#default_value' => 'blat',
+  );
+
+  $form['b']['blat'] = array(
+  	'#type' => 'fieldset',
+  	'#title' => 'BLAT Options',
+  	'#collapsible' => TRUE,
+		'#collapsed' => TRUE,
+  );
+  
+  $form['b']['blat']['min_identity'] = array(
+  	'#type' => 'textfield',
+  	'#title' => 'Minimum Identity',
+  	'#default_value' => '90',
+  );
+  
+  $form['b']['blast'] = array(
+  	'#type' => 'fieldset',
+  	'#title' => 'BLAST Options',
+  	'#collapsible' => TRUE,
+		'#collapsed' => TRUE,
+  );
+  
+  $form['b']['blast']['gapped_alignment'] = array(
+  	'#type' => 'checkbox',
+  	'#title' => 'Gapped Alignment?',
+  	'#default_value' => TRUE,
+  );
+  
+  $form['b']['blast']['evalue'] = array(
+  	'#type' => 'textfield',
+  	'#title' => 'Expectation Values (E-value) Cutoff',
+  	'#description' => 'To enter in scientific notation (ie: 5 x 10-6), enter [base number]e[power] (ie: 5e-6)',
+  	'#default_value' => 10.0
+  );
+  
+  $form['g'] = array(
+  	'#type' => 'fieldset',
+  	'#title' => 'GBrowse Information',
+  );
+  
+  $form['g']['source'] = array(
+  	'#type' => 'textfield',
+  	'#title' => 'Source of Features',
+  	'#description' => 'The source of the features grouped by the selected query library'
+  );
+  
+  //Sending query to the database
+  $resource = db_query('SELECT * FROM {tripal_gbrowse_instances}');
+	$items = array();
+	while($record = db_fetch_object($resource)){
+		$items[$record->gbrowse_id]= $record->gbrowse_name;
+	}
+   
+  //GBrowse Instances
+  $form['g']['gbrowse_id'] = array(
+    '#type' => 'select',
+    '#title' => t('GBrowse Instances'),
+    '#options' => $items,
+    '#description' => t('Selected GBrowse Instances to load the query features into.'),
+  );
+  
+  $form['submit'] = array(
+    '#type' => 'submit',
+    '#name' => 'align',
+    '#value' => 'Align Features',
+  );
+  
+  return $form;
+}
+
+/**
+ * Form submit to initialize an align library tripal job
+ */
+function tripal_gbrowse_align_features_form_submit ($form, &$form_state) {
+  
+  switch($form_state['clicked_button']['#name']) {
+    case 'align':
+      $options = array();
+      // Query
+      if (preg_match('/(L|A)(\d+)/',$form_state['values']['query'], $matches)) {
+        if ($matches[1] == 'L') {
+          $options['query_type'] = 'library';
+        } else {
+          $options['query_type'] = 'analysis';
+        }
+        $options['query_id'] = $matches[2];
+      }
+      
+      // Database
+      if (preg_match('/(L|A)(\d+)/',$form_state['values']['database'], $matches)) {
+        if ($matches[1] == 'L') {
+          $options['db_type'] = 'library';
+        } else {
+          $options['db_type'] = 'analysis';
+        }
+        $options['db_id'] = $matches[2];
+      } 
+      
+      $options['source'] = $form_state['values']['source'];
+      
+      // db options
+      $sql = 'SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id = %d';
+      $r = db_fetch_object(db_query($sql,$form_state['values']['gbrowse_id']));
+      $options['dbname'] = $r->database_name;
+      $options['dbuser'] = $r->database_user;
+      $options['dbpass'] = $r->user_password;
+
+			if ($form_state['values']['program'] == 'blat') { 
+				// blat options
+				$options['min_identity'] = $form_state['values']['min_identity'];
+				
+				global $user;
+				tripal_add_job(
+					'Align '.$options['query_type'].' features ('.$options['query_type'].'_id='.$options['query_id'].')',
+					'tripal_gbrowse',
+					'tripal_gbrowse_align_features_by_blat',
+					array(serialize($options)),
+					$user->uid
+				);			
+			} elseif ($form_state['values']['program'] == 'blast') {      
+				// blast options
+				$options['evalue'] = $form_state['values']['evalue'];
+				$options['gapped_alignment'] = $form_state['values']['gapped_alignment'];
+			
+				global $user;
+				tripal_add_job(
+					'Align '.$options['query_type'].' features ('.$options['query_type'].'_id='.$options['query_id'].')',
+					'tripal_gbrowse',
+					'tripal_gbrowse_align_features_by_blast',
+					array(serialize($options)),
+					$user->uid
+				);
+      }
+      
+    break;
+  }
+}
+
+/**
+ * Aligns feature from a query library/analysis to a database library/analysis,
+ * saving the results as a GFF3 file and then loading it into the selected gbrowse instance
+ *
+ * @param $options
+ *   An array containing options needed to align features and create featurelocs
+ *    -query_type: the type of chado grouping containing query features (either library or analysis)
+ *    -query_id: the library_id/analysis_id containing the query features
+ *    -db_type: the type of chado grouping containing database features (either library or analysis)
+ *    -db_id: the library_id/analysis_id containing the database features
+ *    -dbname: name of the MySQL GBrowse database to load into
+ *    -dbuser: name of the user with permission to load into the above database
+ *    -dbpass: the password for the above user
+ */
+function tripal_gbrowse_align_features_by_blast ($options) {
+  $options = unserialize($options);
+  print 'Query: '.$options['query_type'].' where '.$options['query_type'].'_id='.$options['query_id']."\n";
+  print 'Database: '.$options['db_type'].' where '.$options['db_type'].'_id='.$options['db_id']."\n";
+  
+  // Generate FASTA ---------------------------------------
+  print "\nGenerating fasta files for query and database...\n";
+  $query_file = tripal_gbrowse_export_fasta_for_features( $options['query_type'], $options['query_id'], TRUE );
+  print "\t".$query_file['file']."\n";
+  
+  $db_file = tripal_gbrowse_export_fasta_for_features( $options['db_type'], $options['db_id'], TRUE, TRUE );
+  print "\t".$db_file['file']."\n";
+  
+  // Align using BLAST ------------------------------------
+  print "\nAligning features using BLAST...\n";
+  
+  print "\tFormating Database FASTA into BLASTdb...\n";
+  $db = '/tmp/exported_'.$options['db_type'].'_'.$options['db_id'];
+  $formatdb_cmd = 'formatdb -n '.$db.' -p F -i '.$db_file['file'];
+	print "\t\t".$formatdb_cmd."\n";  
+  exec($formatdb_cmd);
+	
+	print "\tExecuting BLAST...\n";
+	$blast_outfile = $db.'_by_'.$options['query_type'].'_'.$options['query_id'].'.blast.xml';
+	$blastall_cmd = 'blastall -p blastn -d '.$db.' -i '.$query_file['file'].' -m 7 -o '.$blast_outfile.' -e '.$options['evalue'];
+	if ($options['gapped_alignment']) {
+		$blastall_cmd .= ' -g';
+	}
+	print "\t\t".$blastall_cmd."\n";
+	exec($blastall_cmd);
+  
+  // Parse BLAST results ----------------------------------
+  print "\nParsing Blast Results into GFF3...\n";
+  $gff3_file = $db.'_by_'.$options['query_type'].'_'.$options['query_id'].'.gff3';
+  $fgff3 = fopen($gff3_file, 'w');
+  fwrite($fgff3, "##gff-version 3\n");
+  $iteration = tripal_gbrowse_get_next_xml_record ($blast_outfile, "<Iteration>");
+  while ($iteration) {
+  	//print "Record:".$iteration['record']->asXML()."\n";
+  	//print "Query: ".$iteration['record']->{'Iteration_query-def'}."\n";
+		
+		// Find the best Hit by looking at the bit scores of the hsps
+		// the larger the bit score the better the alignment
+		$hits = array();
+		$scores = array();
+  	foreach ($iteration['record']->Iteration_hits->Hit as $hit) {
+  		$score = 0;
+  		$num = 0;
+  		foreach ($hit->{'Hit_hsps'}->{'Hsp'} as $hsp) {
+  			//print 'HSP:'.$hsp->asXML()."\n";
+  			$score = $score + $hsp->{'Hsp_bit-score'};
+  			$num++;
+  		}
+  		$avg = round($score / $num,2);
+  		$hit->{'Hit_bit-score'} = $avg;
+  		$hits[] = array('score' => $avg, 'hit' => $hit);
+  	}
+  	usort($hits, 'tripal_gbrowse_sort_by_score');
+  	$best_hit = $hits[0]['hit'];
+  	//print "\tBest Hit:".$best_hit->Hit_def.' ('.$best_hit->{'Hit_bit-score'}.")\n";
+  	
+  	// generate gff3 for the best hit 
+  	$query_name = $iteration['record']->{'Iteration_query-def'};
+  	$db_name = $best_hit->Hit_def;  
+  	if (isset($db_file['noseq_features'][$db_name])) {
+  	  $db_offset = $db_file['noseq_features'][$db_name]['start'];
+  	  $db_name = $db_file['noseq_features'][$db_name]['parent']['uniquename'];
+  	} else {
+  	  $db_offset = 0;
+  	}
+		$lines = array();
+		$hit_start = 99999999999999999999;
+		$hit_end = 0;
+  	foreach ($best_hit->{'Hit_hsps'}->{'Hsp'} as $hsp) {
+  		if ($hit_start > (int) $hsp->{'Hsp_hit-from'}[0]) { $hit_start = (int) $hsp->{'Hsp_hit-from'}[0]; } 
+  		if ($hit_end < (int) $hsp->{'Hsp_hit-to'}[0]) { $hit_end = (int) $hsp->{'Hsp_hit-to'}; }
+  		$lines[] = implode("\t", array(
+  			$db_name, 
+  			$options['source'],
+  			'match_part',
+  			$hsp->{'Hsp_hit-from'} + $db_offset,
+  			$hsp->{'Hsp_hit-to'} + $db_offset,
+  			$hsp->{'Hsp_bit-score'},
+  			'.',
+  			'.',
+  			'ID='.$query_name.'_'.$hsp->{'Hsp_num'}.';Parent='.$query_name
+  		))."\n";
+  	}
+  	fwrite($fgff3, implode("\t", array(
+			$db_name, 
+			$options['source'],
+			'match',
+			$hit_start + $db_offset,
+			$hit_end + $db_offset,
+			$best_hit->{'Hit_bit-score'},
+			'.',
+			'.',
+			'ID='.$query_name.';Name='.$query_name
+		))."\n");
+		fwrite($fgff3,implode('',$lines));
+  	
+  	// get next iteration xml record
+  	$last_iteration = $iteration;
+  	//print "Getting Iteration...\n";
+  	$iteration = tripal_gbrowse_get_next_xml_record ($blast_outfile, "<Iteration>", $last_iteration['start_line_num']);
+  }
+  
+  print "\nLoading GFF3 into GBrowse...\n";
+  //The loading script: bp_seqfeature_load.pl, allows loading of data to specific file 
+  $command= "bp_seqfeature_load.pl -u '" .$options['dbuser']. "' -p '" .$options['dbpass']. "' -d " .$options['dbname']. " " . $gff3_file;
+  print "\t".$command."\n";
+
+  exec($command);
+}
+
+/**
+ * Aligns feature from a query library/analysis to a database library/analysis,
+ * saving the results as a GFF3 file and then loading it into the selected gbrowse instance
+ *
+ * @param $options
+ *   An array containing options needed to align features and create featurelocs
+ *    -query_type: the type of chado grouping containing query features (either library or analysis)
+ *    -query_id: the library_id/analysis_id containing the query features
+ *    -db_type: the type of chado grouping containing database features (either library or analysis)
+ *    -db_id: the library_id/analysis_id containing the database features
+ *    -dbname: name of the MySQL GBrowse database to load into
+ *    -dbuser: name of the user with permission to load into the above database
+ *    -dbpass: the password for the above user
+ */
+function tripal_gbrowse_align_features_by_blat ($options,$job_id) {
+  $options = unserialize($options);
+  print 'Query: '.$options['query_type'].' where '.$options['query_type'].'_id='.$options['query_id']."\n";
+  print 'Database: '.$options['db_type'].' where '.$options['db_type'].'_id='.$options['db_id']."\n";
+  
+  // Generate FASTA ---------------------------------------
+  print "\nGenerating fasta files for query and database...\n";
+  $query_file = tripal_gbrowse_export_fasta_for_features( $options['query_type'], $options['query_id'], TRUE );
+  print "\t".$query_file['file']."\n";
+  tripal_job_set_progress($job_id, 12);
+  
+  $db_file = tripal_gbrowse_export_fasta_for_features( $options['db_type'], $options['db_id'], TRUE, TRUE );
+  print "\t".$db_file['file']."\n";
+  tripal_job_set_progress($job_id, 25);
+  
+  // Align using BLAT ------------------------------------
+  print "\nAligning features using BLAT...\n";
+	$blat_outfile = '/tmp/alignment_'.$options['db_type'].'-'.$options['db_id'].'_by_'.$options['query_type'].'-'.$options['query_id'].'.psl';
+	$blat_cmd = 'blat '.$db_file['file'].' '.$query_file['file'].' -q=dnax -t=dnax -noHead -minIdentity='.$options['min_identity'].' '.$blat_outfile;
+	print "\t\t".$blat_cmd."\n";
+	exec($blat_cmd);
+	tripal_job_set_progress($job_id, 50);
+	
+	// Parse BLAST results ----------------------------------
+	$total_lines = trim(`wc --lines < $blat_outfile`);
+	$interval = intval($total_lines/5);
+	$percent_per_line = 25/$total_lines;
+	$num_lines = 0;
+	$query_seq = array();
+	
+	print "\nParsing BLAT results into GFF3 (".$total_lines." lines)...\n";
+	$gff3_file = '/tmp/alignment_'.$options['db_type'].'-'.$options['db_id'].'_by_'.$options['query_type'].'-'.$options['query_id'].'.gff3';
+  $fgff3 = fopen($gff3_file, 'w');
+  fwrite($fgff3, "##gff-version 3\n");
+	$bh = fopen($blat_outfile, 'r');
+	while (!feof($bh)) {
+		$line = explode("\t", fgets($bh));
+		$num_lines++;
+		if (($num_lines%$interval) == 0) { tripal_job_set_progress($job_id, intval($percent_per_line * $num_lines)); }
+		
+		$print_match = TRUE;
+    $db_name = $line[13];
+  	if (isset($db_file['noseq_features'][$db_name])) {
+  	  $db_offset = $db_file['noseq_features'][$db_name]['start'];
+  	  $db_name = $db_file['noseq_features'][$db_name]['parent']['uniquename'];
+  	} else {
+  	  $db_offset = 0;
+  	}
+  	
+  	$query_id = $line[9];
+  	if (!isset($query_seq[ $line[9] ])) {
+  		$query_seq[ $line[9] ]['id'] = 0;
+  		$query_seq[ $line[9] ]['start'] = $line[15] + $db_offset;
+  		$query_seq[ $line[9] ]['end'] = $line[16] + $db_offset;
+  		$query_id .= '_0';
+  	} elseif ( abs($line[15]+$db_offset-$query_seq[ $line[9] ]['start']) < 5 ) {
+  		$print_match = FALSE;
+  		$query_id .= '_' . $query_seq[ $line[9] ]['id'];
+  	}else {
+  		$query_seq[ $line[9] ]['id']++;
+  		$query_id .= '_' . $query_seq[ $line[9] ]['id'];
+  	}
+  	
+		// match line
+		if ($print_match) {
+			fwrite($fgff3, implode("\t", array(
+				$db_name, 
+				$options['source'],
+				'match',
+				$line[15] + $db_offset,
+				$line[16] + $db_offset,
+				'.',
+				$line[8][1],
+				'.',
+				'ID='.$query_id.';Name='.$line[9]
+			))."\n");
+		}
+		
+		// match parts
+		$parts_size = explode(',',trim($line[18]));
+		$parts_start = explode(',',trim($line[20]));
+		foreach ($parts_size as $k => $length) {
+
+			if (!empty($parts_start[$k])) {
+				fwrite($fgff3, implode("\t", array(
+					$db_name, 
+					$options['source'],
+					'match_part',
+					$parts_start[$k] + $db_offset,
+					$parts_start[$k] + $length + $db_offset,
+					'.',
+					$line[8][1],
+					'.',
+					'ID='.$query_id.'_'.$k.';Parent='.$query_id
+				))."\n");
+  		}
+  		
+		}
+	}
+	tripal_job_set_progress($job_id, 75);
+	
+	// Load into GBrowse ------------------------------------
+  print "\nLoading GFF3 into GBrowse...\n";
+  //The loading script: bp_seqfeature_load.pl, allows loading of data to specific file 
+  $command= "bp_seqfeature_load.pl -u '" .$options['dbuser']. "' -p '" .$options['dbpass']. "' -d " .$options['dbname']. " " . $gff3_file;
+  print "\t".$command."\n";
+	exec($command);
+
+}
+
+/**
+ * Creates a fasta file for a given chado grouping of features
+ *
+ * @param $type
+ *   The type of chado grouping. Allowed values are either library or analysis
+ * @param $id
+ *   The library_id/analysis_id of the chado grouping
+ * @return
+ *   The name of the multi-fasta file containing records for all features with residues
+ *   in the supplied library/analysis
+ */
+function tripal_gbrowse_export_fasta_for_features ($type, $id, $use_parent_seq = FALSE, $save_offset = FALSE) {
+
+  $fasta_file = '/tmp/exported_fasta-'.$type.'-'.$id.'.fasta';
+  $noseq_features = array();
+  
+  $fh = fopen($fasta_file,'w');
+  
+  $sql = 'SELECT f.uniquename, f.residues, fl.fmin, fl.fmax, fl.srcfeature_id as parent_feature_id FROM feature f '
+  	.'LEFT JOIN featureloc fl ON fl.feature_id=f.feature_id ';
+  $parent_sql = 'SELECT p.feature_id as parent_feature_id, p.uniquename as parent_uniquename, count(fl.feature_id) FROM feature p '
+  	.'LEFT JOIN featureloc fl ON fl.srcfeature_id=p.feature_id '
+  	."WHERE fl.feature_id IN (SELECT feature_id FROM feature WHERE residues='') AND ";
+  if ($type == 'library') { 
+  	$sql .= 'LEFT JOIN library_feature lf ON f.feature_id=lf.feature_id WHERE lf.library_id=%d';
+  	$parent_sql .= 'fl.feature_id IN (SELECT feature_id FROM library_feature WHERE library_id=%d) GROUP BY p.uniquename, p.feature_id';
+    
+  } elseif ($type == 'analysis') {
+  	$sql .= 'LEFT JOIN analysisfeature af ON f.feature_id=af.feature_id WHERE af.analysis_id=%d';
+		$parent_sql .= 'fl.feature_id IN (SELECT feature_id FROM analysisfeature WHERE analysis_id=%d) GROUP BY p.uniquename, p.feature_id';
+    $resource = db_query($sql, $id);
+  } else {
+    print "ERROR: Unable to generate FASTA due to unrecognized type -".$type."!\n";
+    return FALSE;
+  }
+
+  
+  // check if some don't have sequence but are aligned on a parent who does
+	//print "SQL: ".$parent_sql."\n";
+  $resource = db_query($parent_sql, $id);
+	$parent_seq = array();
+	$residues_seq = 'SELECT residues FROM feature WHERE feature_id=%d';
+  while ($r = db_fetch_object($resource)) {
+  	//print 'Creating index for '.$r->parent_feature_id. " (".$r->parent_uniquename.")\n";
+  	$seq = db_fetch_object(db_query($residues_seq, $r->parent_feature_id));
+  	//print "Residues:".$seq->residues."\n";
+  	if (!empty($seq->residues)) {
+	  	//print "\tGot Seq!\n";
+	  }
+		$parent_seq[ $r->parent_feature_id ] = array(
+			'residues' => $seq->residues,
+			'uniquename' => $r->parent_uniquename
+		);
+  }
+  
+	$resource = db_query($sql, $id);
+  while ($r = db_fetch_object($resource)) {
+    if (!empty($r->residues)) {
+      fwrite($fh, '>'.$r->uniquename."\n");
+      fwrite($fh, wordwrap($r->residues,80,"\n",TRUE)."\n");
+    } else {
+	    //print $r->uniquename." (based on ".$r->parent_feature_id.' -'.$parent_seq[$r->parent_feature_id]['uniquename'].")\n";
+      if (!empty($parent_seq[$r->parent_feature_id]['residues'])) {
+      	//print "\tHave Seq\n";
+      	fwrite($fh, '>'.$r->uniquename." (based on ".$parent_seq[$r->parent_feature_id]['uniquename'].")\n");
+        $seq = substr($parent_seq[$r->parent_feature_id]['residues'], $r->fmin, $r->fmax - $r->fmin);
+        fwrite($fh, wordwrap($seq,80,"\n",TRUE)."\n");
+        if ($save_offset) {
+          $noseq_features[ $r->uniquename ] = array(
+            'start' => $r->fmin,
+            'end' => $r->fmax,
+            'parent' => array(
+              'uniquename' => $parent_seq[$r->parent_feature_id]['uniquename'],
+            ),
+          );
+        }
+      }
+    }
+  }
+  
+  fclose($fh);
+  return array(
+    'file' => $fasta_file,
+    'noseq_features' => $noseq_features
+  );
+}
+
+/**
+ * Retrieves the next xml record with $record_identifier
+ *
+ * Assumption: the end tag for $record_identifier is one line before the next opening tag
+ * @param $xml_file
+ *   The file containing the xml records; must supply the full path
+ * @param $record_identifier
+ *   The opening tag enclosing a record (ie: <Iteration>)
+ * @param $last_record_line_num
+ *   The line number of the openin tag for the last record
+ * 
+ * @return
+ *   An array describing the next xml record
+ *    -record: the simpleXML record
+ *    -start_line_num: the line number in the file that this record starts at
+ *    -end_line_num: the line number in the file that this record ends at
+ */
+function tripal_gbrowse_get_next_xml_record ($xml_file, $record_identifier, $last_record_line_num = NULL) {
+
+	// If first record ------------------------------------------------
+	if (!$last_record_line_num) {
+		$cmd = 'grep -n "'.$record_identifier.'" -m 2 '.$xml_file;
+		exec($cmd, $line_num_raw);
+
+		// get start of next record
+		if (preg_match('/(\d+):.*/',$line_num_raw[0],$matches)) {
+			$start = $matches[1];
+		} else {
+			return FALSE;
+		}
+
+		// get end of next record
+		if (preg_match('/(\d+):.*/',$line_num_raw[1],$matches)) {
+			$end = $matches[1] -1;
+		} else {
+			return FALSE;
+		}
+
+	// If not first record --------------------------------------------
+	} else {
+
+		$cmd = 'tail --lines=+'.($last_record_line_num+1).' '.$xml_file.' 2>/dev/null | grep -n "'.$record_identifier.'" -m 2 2>/dev/null ';
+		exec($cmd, $line_num_raw);
+
+		// get start of next record
+		if (preg_match('/(\d+):.*/',$line_num_raw[0],$matches)) {
+			$start = $matches[1] + $last_record_line_num;
+		} else {
+			return FALSE;
+		}
+
+		// get end of next record
+		if (preg_match('/(\d+):.*/',$line_num_raw[1],$matches)) {
+			$end = $matches[1] + $last_record_line_num -1;
+		} else {
+			return FALSE;
+		}
+		
+	}
+	
+	$cmd = 'tail --lines=+'.$start.' '.$xml_file.' 2>/dev/null | head -n '.($end-$start+1).' 2>/dev/null';
+	exec($cmd, $xml);
+	
+	//print "XML:".implode("\n",$xml)."\n";
+	if (!$xml) {
+		return FALSE;
+	}
+	
+	$xml_record = new SimpleXMLElement(implode("\n",$xml));
+	return array(
+		'record' => $xml_record,
+		'start_line_num' => $start,
+		'end_line_num' => $end,
+	);
+}
+
+/**
+ * Custom sort function to be used with usort
+ * Sorts an array( 'score' => \d+, 'hit' => simplexml obj)
+ */
+function tripal_gbrowse_sort_by_score ($a, $b) {
+
+	if ($a['score'] == $b['score']) {
+		return 0;
+	} elseif ($a['score'] < $b['score']) {
+		return 1;
+	} else {
+		return -1;
+	}
+}

tripal_gbrowse/tripal_gbrowse.module

@@ -11,6 +11,7 @@
  * multiple GBrowse/mysql instances as well as manage and create such GBrowse instances
  */
 
+include('tripal_gbrowse.align_features.inc');
 
 //-----------------------------------------------------------------------------
 //  SECTION: Main Outline Menu for GBrowse Management 
@@ -121,6 +122,15 @@ function tripal_gbrowse_menu() {
       'access arguments' => array('administer site configuration'),
       'type' => MENU_NORMAL_ITEM
   );
+  
+  $items['admin/tripal/tripal_gbrowse/align_features']=array(
+      'title' => t('Align Features'),
+      'description' => t('Align a group of features (either library or analysis) against another grouping of features.'), 
+      'page callback' => 'drupal_get_form',
+      'page arguments' => array('tripal_gbrowse_align_features_form'), 
+      'access arguments' => array('administer site configuration'),
+      'type' => MENU_NORMAL_ITEM
+  );  
 
   return $items;
 }
@@ -271,6 +281,7 @@ function tripal_gbrowse_administration_description_page() {
   $text .= "<ul>";
   
   $text .= "<li>".l("Configuration", "admin/tripal/tripal_gbrowse/configuration"). "</li>";
+	$text .= "<li>".l('Register GBrowse Instance', 'node/add/tripal-gbrowse')."</li>";
   $text .= "<li>".l("Load Library Features", "admin/tripal/tripal_gbrowse/load_library_features"). "</li>";
   $text .= "<li>".l("Delete Library Features", "admin/tripal/tripal_gbrowse/delete_library_features"). "</li>";
   $text .= "<li>".l("Load Analysis Features", "admin/tripal/tripal_gbrowse/load_analysis_features"). "</li>";
@@ -684,7 +695,7 @@ function tripal_gbrowse_form(&$node, $form_state) {
     '#type' => 'textfield',
     '#title' => t('GBrowse Name'),
     '#size' => 30,
-    '#maxlength' => 64,
+    '#maxlength' => 256,
     '#description' => t('GBrowse Instance'),
     '#default_value' => isset($node->gbrowse->gbrowse_name) ? $node->gbrowse->gbrowse_name : '',
     '#required' => TRUE,
@@ -698,7 +709,7 @@ function tripal_gbrowse_form(&$node, $form_state) {
     '#type' => 'textfield',
     '#title' => t('GBrowse Link'),
     '#size' => 30,
-    '#maxlength' => 64,
+    '#maxlength' => 256,
     '#description'=>t('Enter Full HTML address Including Host 
     (ex:http://knowpulse2.usask.ca/) of the new GBrowse instance. By default this is '.$default_value.'[configuration file name] where the configuration file name is the same as that entered below except without .conf'),
     '#default_value' => isset($node->gbrowse->gbrowse_link) ? $node->gbrowse->gbrowse_link : $default_value,
@@ -710,7 +721,7 @@ function tripal_gbrowse_form(&$node, $form_state) {
     '#type' => 'textfield',
     '#title' => t('Configuration File'),
     '#size' => 30,
-    '#maxlength' => 64,
+    '#maxlength' => 256,
     '#description' => t('Enter Fully Qualified File Name including Path (ex: file.conf) '),
     '#default_value' => isset($node->gbrowse->config_file) ? $node->gbrowse->config_file : variable_get('tripal_gbrowse_configuration_file_path', ''),
     '#required' => TRUE,
@@ -768,6 +779,16 @@ function tripal_gbrowse_form(&$node, $form_state) {
   
 }
 
+function tripal_gbrowse_validate ($node, $form) {
+
+  if (!preg_match('/\.conf$/',$node->config_file)) {
+    form_set_error('config_file','Configuration file must end in .conf');
+  }
+  
+  if (!preg_match('/^http:\/\//',$node->gbrowse_link)) {
+    form_set_error('gbrowse_link','GBrowse Link must be an absolute path (include http://)');
+  }
+}
 
 /**
  *  Implements tripal_gbrowse_help()