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@@ -0,0 +1,647 @@
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+<?php
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+
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+/**
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+ * Form to initialize an align library tripal job
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+ */
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+function tripal_gbrowse_align_features_form ($form_state) {
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+ $form = array();
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+
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+ // compile all analysis' as options
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+ $analysis_options = array();
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+ $results = tripal_core_chado_select('analysis',array('analysis_id','name', 'program'), array());
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+ foreach ($results as $r) {
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+ $analysis_options[ 'A'.$r->analysis_id ] = $r->name .' --'.$r->program;
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+ }
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+
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+ // compile all libraries as options
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+ $library_options = array();
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+ $results = tripal_core_chado_select('library',array('library_id','name', 'uniquename'), array());
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+ foreach ($results as $r) {
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+ $library_options[ 'L'.$r->library_id ] = $r->name .' --'.$r->uniquename;
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+ }
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+
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+ $form['description'] = array(
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+ '#type' => 'item',
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+ '#value' => 'This form allows you to select a query library/analysis and align the '
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+ .'features that are part of that query library/analysis against those from a database '
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+ .'library/analysis using BLAST. Depending upon the Alignment Criteria, the top BLAST '
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+ .'result(s) for each query feature will be used to determine the location of the query '
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+ .'feature on a database feature.',
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+ );
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+
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+ $form['q'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => 'Features to be Aligned (Query)',
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+ '#description' => 'Please select the library or analysis below which groups the features you '
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+ .'want aligned together.',
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+ );
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+
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+ $form['q']['query'] = array(
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+ '#type' => 'select',
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+ '#title' => 'Query Features',
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+ '#options' => array(
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+ 'Libraries' => $library_options,
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+ "Analaysis'" => $analysis_options
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+ ),
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+ '#default_value' => $form_state['values']['query'],
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+ );
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+
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+ $form['d'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => 'Features to Align To (Database)',
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+ '#description' => 'Please select the library of analysis below, which contains the features '
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+ .'you want to align the query features selected above to. Only features in the selected '
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+ .'library/analysis with sequence data will be used.',
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+ );
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+
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+ $form['d']['database'] = array(
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+ '#type' => 'select',
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+ '#title' => 'Database Features',
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+ '#options' => array(
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+ 'Libraries' => $library_options,
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+ "Analaysis'" => $analysis_options
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+ ),
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+ '#default_value' => $form_state['values']['database'],
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+ );
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+
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+ $form['b'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => 'Alignment Criteria',
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+ );
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+
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+ $form['b']['program'] = array(
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+ '#type' => 'radios',
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+ '#title' => 'Alignment Program',
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+ '#options' => array(
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+ 'blast' => 'BLAST',
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+ 'blat' => 'BLAT',
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+ ),
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+ '#default_value' => 'blat',
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+ );
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+
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+ $form['b']['blat'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => 'BLAT Options',
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+ '#collapsible' => TRUE,
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+ '#collapsed' => TRUE,
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+ );
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+
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+ $form['b']['blat']['min_identity'] = array(
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+ '#type' => 'textfield',
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+ '#title' => 'Minimum Identity',
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+ '#default_value' => '90',
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+ );
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+
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+ $form['b']['blast'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => 'BLAST Options',
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+ '#collapsible' => TRUE,
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+ '#collapsed' => TRUE,
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+ );
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+
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+ $form['b']['blast']['gapped_alignment'] = array(
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+ '#type' => 'checkbox',
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+ '#title' => 'Gapped Alignment?',
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+ '#default_value' => TRUE,
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+ );
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+
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+ $form['b']['blast']['evalue'] = array(
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+ '#type' => 'textfield',
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+ '#title' => 'Expectation Values (E-value) Cutoff',
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+ '#description' => 'To enter in scientific notation (ie: 5 x 10-6), enter [base number]e[power] (ie: 5e-6)',
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+ '#default_value' => 10.0
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+ );
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+
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+ $form['g'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => 'GBrowse Information',
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+ );
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+
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+ $form['g']['source'] = array(
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+ '#type' => 'textfield',
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+ '#title' => 'Source of Features',
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+ '#description' => 'The source of the features grouped by the selected query library'
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+ );
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+
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+ //Sending query to the database
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+ $resource = db_query('SELECT * FROM {tripal_gbrowse_instances}');
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+ $items = array();
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+ while($record = db_fetch_object($resource)){
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+ $items[$record->gbrowse_id]= $record->gbrowse_name;
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+ }
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+
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+ //GBrowse Instances
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+ $form['g']['gbrowse_id'] = array(
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+ '#type' => 'select',
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+ '#title' => t('GBrowse Instances'),
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+ '#options' => $items,
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+ '#description' => t('Selected GBrowse Instances to load the query features into.'),
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+ );
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+
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+ $form['submit'] = array(
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+ '#type' => 'submit',
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+ '#name' => 'align',
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+ '#value' => 'Align Features',
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+ );
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+
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+ return $form;
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+}
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+
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+/**
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+ * Form submit to initialize an align library tripal job
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+ */
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+function tripal_gbrowse_align_features_form_submit ($form, &$form_state) {
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+
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+ switch($form_state['clicked_button']['#name']) {
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+ case 'align':
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+ $options = array();
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+ // Query
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+ if (preg_match('/(L|A)(\d+)/',$form_state['values']['query'], $matches)) {
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+ if ($matches[1] == 'L') {
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+ $options['query_type'] = 'library';
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+ } else {
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+ $options['query_type'] = 'analysis';
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+ }
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+ $options['query_id'] = $matches[2];
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+ }
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+
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+ // Database
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+ if (preg_match('/(L|A)(\d+)/',$form_state['values']['database'], $matches)) {
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+ if ($matches[1] == 'L') {
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+ $options['db_type'] = 'library';
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+ } else {
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+ $options['db_type'] = 'analysis';
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+ }
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+ $options['db_id'] = $matches[2];
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+ }
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+
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+ $options['source'] = $form_state['values']['source'];
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+
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+ // db options
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+ $sql = 'SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id = %d';
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+ $r = db_fetch_object(db_query($sql,$form_state['values']['gbrowse_id']));
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+ $options['dbname'] = $r->database_name;
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+ $options['dbuser'] = $r->database_user;
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+ $options['dbpass'] = $r->user_password;
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+
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+ if ($form_state['values']['program'] == 'blat') {
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+ // blat options
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+ $options['min_identity'] = $form_state['values']['min_identity'];
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+
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+ global $user;
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+ tripal_add_job(
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+ 'Align '.$options['query_type'].' features ('.$options['query_type'].'_id='.$options['query_id'].')',
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+ 'tripal_gbrowse',
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+ 'tripal_gbrowse_align_features_by_blat',
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+ array(serialize($options)),
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+ $user->uid
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+ );
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+ } elseif ($form_state['values']['program'] == 'blast') {
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+ // blast options
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+ $options['evalue'] = $form_state['values']['evalue'];
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+ $options['gapped_alignment'] = $form_state['values']['gapped_alignment'];
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+
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+ global $user;
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+ tripal_add_job(
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+ 'Align '.$options['query_type'].' features ('.$options['query_type'].'_id='.$options['query_id'].')',
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+ 'tripal_gbrowse',
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+ 'tripal_gbrowse_align_features_by_blast',
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+ array(serialize($options)),
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+ $user->uid
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+ );
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+ }
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+
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+ break;
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+ }
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+}
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+
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+/**
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+ * Aligns feature from a query library/analysis to a database library/analysis,
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+ * saving the results as a GFF3 file and then loading it into the selected gbrowse instance
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+ *
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+ * @param $options
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+ * An array containing options needed to align features and create featurelocs
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+ * -query_type: the type of chado grouping containing query features (either library or analysis)
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+ * -query_id: the library_id/analysis_id containing the query features
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+ * -db_type: the type of chado grouping containing database features (either library or analysis)
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+ * -db_id: the library_id/analysis_id containing the database features
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+ * -dbname: name of the MySQL GBrowse database to load into
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+ * -dbuser: name of the user with permission to load into the above database
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+ * -dbpass: the password for the above user
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+ */
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+function tripal_gbrowse_align_features_by_blast ($options) {
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+ $options = unserialize($options);
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+ print 'Query: '.$options['query_type'].' where '.$options['query_type'].'_id='.$options['query_id']."\n";
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+ print 'Database: '.$options['db_type'].' where '.$options['db_type'].'_id='.$options['db_id']."\n";
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+
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+ // Generate FASTA ---------------------------------------
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+ print "\nGenerating fasta files for query and database...\n";
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+ $query_file = tripal_gbrowse_export_fasta_for_features( $options['query_type'], $options['query_id'], TRUE );
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+ print "\t".$query_file['file']."\n";
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+
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+ $db_file = tripal_gbrowse_export_fasta_for_features( $options['db_type'], $options['db_id'], TRUE, TRUE );
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+ print "\t".$db_file['file']."\n";
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+
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+ // Align using BLAST ------------------------------------
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+ print "\nAligning features using BLAST...\n";
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+
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+ print "\tFormating Database FASTA into BLASTdb...\n";
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+ $db = '/tmp/exported_'.$options['db_type'].'_'.$options['db_id'];
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+ $formatdb_cmd = 'formatdb -n '.$db.' -p F -i '.$db_file['file'];
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+ print "\t\t".$formatdb_cmd."\n";
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+ exec($formatdb_cmd);
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+
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+ print "\tExecuting BLAST...\n";
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+ $blast_outfile = $db.'_by_'.$options['query_type'].'_'.$options['query_id'].'.blast.xml';
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+ $blastall_cmd = 'blastall -p blastn -d '.$db.' -i '.$query_file['file'].' -m 7 -o '.$blast_outfile.' -e '.$options['evalue'];
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+ if ($options['gapped_alignment']) {
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+ $blastall_cmd .= ' -g';
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+ }
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+ print "\t\t".$blastall_cmd."\n";
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+ exec($blastall_cmd);
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+
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+ // Parse BLAST results ----------------------------------
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+ print "\nParsing Blast Results into GFF3...\n";
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+ $gff3_file = $db.'_by_'.$options['query_type'].'_'.$options['query_id'].'.gff3';
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+ $fgff3 = fopen($gff3_file, 'w');
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+ fwrite($fgff3, "##gff-version 3\n");
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+ $iteration = tripal_gbrowse_get_next_xml_record ($blast_outfile, "<Iteration>");
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+ while ($iteration) {
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+ //print "Record:".$iteration['record']->asXML()."\n";
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+ //print "Query: ".$iteration['record']->{'Iteration_query-def'}."\n";
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+
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+ // Find the best Hit by looking at the bit scores of the hsps
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+ // the larger the bit score the better the alignment
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+ $hits = array();
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+ $scores = array();
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+ foreach ($iteration['record']->Iteration_hits->Hit as $hit) {
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+ $score = 0;
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+ $num = 0;
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+ foreach ($hit->{'Hit_hsps'}->{'Hsp'} as $hsp) {
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+ //print 'HSP:'.$hsp->asXML()."\n";
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+ $score = $score + $hsp->{'Hsp_bit-score'};
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+ $num++;
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+ }
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+ $avg = round($score / $num,2);
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+ $hit->{'Hit_bit-score'} = $avg;
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+ $hits[] = array('score' => $avg, 'hit' => $hit);
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+ }
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+ usort($hits, 'tripal_gbrowse_sort_by_score');
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+ $best_hit = $hits[0]['hit'];
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+ //print "\tBest Hit:".$best_hit->Hit_def.' ('.$best_hit->{'Hit_bit-score'}.")\n";
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+
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+ // generate gff3 for the best hit
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+ $query_name = $iteration['record']->{'Iteration_query-def'};
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+ $db_name = $best_hit->Hit_def;
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+ if (isset($db_file['noseq_features'][$db_name])) {
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+ $db_offset = $db_file['noseq_features'][$db_name]['start'];
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+ $db_name = $db_file['noseq_features'][$db_name]['parent']['uniquename'];
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+ } else {
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+ $db_offset = 0;
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+ }
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+ $lines = array();
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+ $hit_start = 99999999999999999999;
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+ $hit_end = 0;
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+ foreach ($best_hit->{'Hit_hsps'}->{'Hsp'} as $hsp) {
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+ if ($hit_start > (int) $hsp->{'Hsp_hit-from'}[0]) { $hit_start = (int) $hsp->{'Hsp_hit-from'}[0]; }
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+ if ($hit_end < (int) $hsp->{'Hsp_hit-to'}[0]) { $hit_end = (int) $hsp->{'Hsp_hit-to'}; }
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+ $lines[] = implode("\t", array(
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+ $db_name,
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+ $options['source'],
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+ 'match_part',
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+ $hsp->{'Hsp_hit-from'} + $db_offset,
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+ $hsp->{'Hsp_hit-to'} + $db_offset,
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+ $hsp->{'Hsp_bit-score'},
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+ '.',
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+ '.',
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+ 'ID='.$query_name.'_'.$hsp->{'Hsp_num'}.';Parent='.$query_name
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+ ))."\n";
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+ }
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+ fwrite($fgff3, implode("\t", array(
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+ $db_name,
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+ $options['source'],
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+ 'match',
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+ $hit_start + $db_offset,
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+ $hit_end + $db_offset,
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+ $best_hit->{'Hit_bit-score'},
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+ '.',
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+ '.',
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+ 'ID='.$query_name.';Name='.$query_name
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+ ))."\n");
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+ fwrite($fgff3,implode('',$lines));
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+
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+ // get next iteration xml record
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+ $last_iteration = $iteration;
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+ //print "Getting Iteration...\n";
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+ $iteration = tripal_gbrowse_get_next_xml_record ($blast_outfile, "<Iteration>", $last_iteration['start_line_num']);
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+ }
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+
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+ print "\nLoading GFF3 into GBrowse...\n";
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+ //The loading script: bp_seqfeature_load.pl, allows loading of data to specific file
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+ $command= "bp_seqfeature_load.pl -u '" .$options['dbuser']. "' -p '" .$options['dbpass']. "' -d " .$options['dbname']. " " . $gff3_file;
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+ print "\t".$command."\n";
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+
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+ exec($command);
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+}
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+
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+/**
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+ * Aligns feature from a query library/analysis to a database library/analysis,
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+ * saving the results as a GFF3 file and then loading it into the selected gbrowse instance
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+ *
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+ * @param $options
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+ * An array containing options needed to align features and create featurelocs
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+ * -query_type: the type of chado grouping containing query features (either library or analysis)
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+ * -query_id: the library_id/analysis_id containing the query features
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+ * -db_type: the type of chado grouping containing database features (either library or analysis)
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+ * -db_id: the library_id/analysis_id containing the database features
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+ * -dbname: name of the MySQL GBrowse database to load into
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+ * -dbuser: name of the user with permission to load into the above database
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+ * -dbpass: the password for the above user
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+ */
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+function tripal_gbrowse_align_features_by_blat ($options,$job_id) {
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+ $options = unserialize($options);
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+ print 'Query: '.$options['query_type'].' where '.$options['query_type'].'_id='.$options['query_id']."\n";
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+ print 'Database: '.$options['db_type'].' where '.$options['db_type'].'_id='.$options['db_id']."\n";
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+
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+ // Generate FASTA ---------------------------------------
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+ 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;
|
|
|
+ }
|
|
|
+}
|
laceysanderson