<?php
require_once "gaf_loader.inc";
function tripal_analysis_go_init(){
// Add style sheet
drupal_add_css(drupal_get_path('theme', 'tripal').'/css/tripal_analysis_go.css');
drupal_add_js(drupal_get_path('theme', 'tripal').'/js/tripal_analysis_go.js');
}
/*******************************************************************************
* Menu items are automatically added for the new node types created
* by this module to the 'Create Content' Navigation menu item. This function
* adds more menu items needed for this module.
*/
function tripal_analysis_go_menu() {
$items = array();
$items['download_goterm_features'] = array(
'path' => 'download_goterm_features',
'title' => t('Get GO Term Features'),
'page callback' => 'tripal_analysis_go_get_goterm_features',
'page arguments' => array(1,2),
'access arguments' => array('access chado_analysis_go content'),
'type' => MENU_CALLBACK
);
$items['tripal_analysis_go_org_charts'] = array(
'path' => 'tripal_analysis_go_org_charts',
'title' => t('Analysis GO Charts'),
'page callback' => 'tripal_analysis_go_org_charts',
'page arguments' => array(1),
'access arguments' => array('access chado_analysis_go content'),
'type' => MENU_CALLBACK
);
$items['admin/tripal/tripal_analysis_go'] = array(
'title' => 'Gene Ontology',
'description' => 'Administrative tools for managing Gene Ontology data.',
'page callback' => 'tripal_analysis_go_module_description_page',
'access arguments' => array('administer site configuration'),
'type' => MENU_NORMAL_ITEM,
);
$items['admin/tripal/tripal_analysis_go/gaf_load'] = array(
'title' => t('Import GO terms with GAF file'),
'description' => t("Import GO terms into Chado using the Gene Ontology's GAF 2.0 file format"),
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_analysis_go_gaf_load_form'),
'access arguments' => array('access administration pages'),
'type' => MENU_NORMAL_ITEM,
);
return $items;
}
/*************************************************************************
* Purpose: Provide Guidance to new Tripal Admin
*
* @return HTML Formatted text
*/
function tripal_analysis_go_module_description_page() {
$text = '';
$text .= '<h3>Description:</h3>';
$text .= '<p>TODO: Basic Description of this module including mention/link to the chado module</p>';
$text .= '<h3>Post Installation Instructions:</h3>';
$text .= '<p>TODO: Describe any post installation intructions here. You shouldalways include setting user permissions.</p>';
$text .= '<h3>Features of this Module:</h3>';
$text .= '<p>TODO: Discuss the Features of this module including links. Some features to consider are creating content, details pages/node content, editing/deleteing, basic listings and vies integration. See admin/tripal/tripal_stock for an example.</p>';
return $text;
}
/*******************************************************************************
* Set the permission types that the chado module uses. Essentially we
* want permissionis that protect creation, editing and deleting of chado
* data objects
*/
function tripal_analysis_go_perm(){
return array(
'access chado_analysis_go content',
'create chado_analysis_go content',
'delete chado_analysis_go content',
'edit chado_analysis_go content',
);
}
/*******************************************************************************
* The following function proves access control for users trying to
* perform actions on data managed by this module
*/
function chado_analysis_go_access($op, $node, $account){
if ($op == 'create') {
return user_access('create chado_analysis_go content', $account);
}
if ($op == 'update') {
if (user_access('edit chado_analysis_go content', $account)) {
return TRUE;
}
}
if ($op == 'delete') {
if (user_access('delete chado_analysis_go content', $account)) {
return TRUE;
}
}
if ($op == 'view') {
if (user_access('access chado_analysis_go content', $account)) {
return TRUE;
}
}
return FALSE;
}
/*******************************************************************************
*
*/
function tripal_analysis_go_block($op = 'list', $delta = 0, $edit=array()){
switch($op) {
case 'list':
$blocks['tago_org_sum']['info'] = t('Tripal Organism GO Analysis Report');
$blocks['tago_org_sum']['cache'] = BLOCK_NO_CACHE;
$blocks['featurego']['info'] = t('Tripal Feature GO Terms');
$blocks['featurego']['cache'] = BLOCK_NO_CACHE;
return $blocks;
case 'view':
if(user_access('access chado_analysis_go content') and arg(0) == 'node' and is_numeric(arg(1))) {
$nid = arg(1);
$node = node_load($nid);
$block = array();
switch($delta){
case 'tago_org_sum':
$block['subject'] = t('GO Summary');
$block['content'] = theme('tripal_organism_go_summary',$node);
break;
case 'featurego':
$block['subject'] = t('GO Terms');
$block['content'] = theme('tripal_feature_go_terms',$node);
break;
default :
}
return $block;
}
}
}
/*******************************************************************************
* HOOK: Implementation of hook_nodeapi()
* Display library information for associated features or organisms
* This function also provides contents for indexing
*/
function tripal_analysis_go_nodeapi(&$node, $op, $teaser, $page) {
switch ($op) {
case 'view':
if ($teaser) {
return;
}
// add the library to the organism/feature search indexing
if($node->build_mode == NODE_BUILD_SEARCH_INDEX){
$node->content['tripal_analysis_go_search_index'] = array(
'#value' => theme('tripal_analysis_go_search_index',$node),
'#weight' => 5,
);
} else if ($node->build_mode == NODE_BUILD_SEARCH_RESULT) {
$node->content['tripal_analysis_go_search_result'] = array(
'#value' => theme('tripal_analysis_go_search_result',$node),
'#weight' => 5,
);
} else {
// Show go terms if the organism/feature is not at teaser view
switch($node->type){
case 'chado_organism':
$node->content['tripal_organism_go_summary'] = array(
'#value' => theme('tripal_organism_go_summary',$node),
'#weight' => 5,
);
break;
case 'chado_feature':
$node->content['tripal_feature_go_terms'] = array(
'#value' => theme('tripal_feature_go_terms',$node),
'#weight' => 5,
);
break;
}
}
break;
}
}
/************************************************************************
* We need to let drupal know about our theme functions and their arguments.
* We create theme functions to allow users of the module to customize the
* look and feel of the output generated in this module
*/
function tripal_analysis_go_theme () {
return array(
'tripal_analysis_go_search_index' => array (
'arguments' => array('node'),
),
'tripal_analysis_go_search_result' => array (
'arguments' => array('node'),
),
'tripal_organism_go_summary' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_organism_go_summary',
),
'tripal_feature_go_terms' => array (
'arguments' => array('node'=> null),
'template' => 'tripal_feature_go_terms',
)
);
}
/************************************************************************
*/
function theme_tripal_analysis_go_search_index($node){
}
/************************************************************************
*/
function theme_tripal_analysis_go_search_result($node){
}
/************************************************************************
*/
function tripal_analysis_go_preprocess_tripal_feature_go_terms(&$variables){
$feature = $variables['node']->feature;
$feature->tripal_analysis_go->terms = tripal_analysis_go_load_feature_terms($feature);
}
/************************************************************************
*/
function tripal_analysis_go_preprocess_tripal_organism_go_summary(&$variables){
$node = $variables['node'];
$organism = $node->organism;
$organism->tripal_analysis_go->select_form = tripal_analysis_go_load_organism_go_summary($node);
}
/************************************************************************
*/
function tripal_analysis_go_select_form(&$form_state = NULL,$node){
$form = array();
// find analyses that have GO terms
$sql = "
SELECT DISTINCT A.analysis_id, A.name, GCA.organism_id
FROM {go_count_analysis} GCA
INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id
WHERE organism_id = %d
ORDER BY analysis_id DESC
";
$previous_db = tripal_db_set_active('chado');
$results = db_query($sql,$node->organism->organism_id);
tripal_db_set_active($previous_db);
$analyses = array();
$analyses[''] = '';
while($analysis = db_fetch_object($results)){
$analyses[$analysis->analysis_id."-".$analysis->organism_id] = "$analysis->name";
}
# create the select box
$form['tripal_analysis_go_select'] = array(
'#title' => t('Select a GO report to view'),
'#description' => t('Any analysis with GO results related to this organism are available for viewing. For further information, see the analysis information page.'),
'#type' => 'select',
'#options' => $analyses,
'#attributes' => array (
'onchange' => 'tripal_analysis_go_org_charts(this.options[this.selectedIndex].value)'
),
);
return $form;
}
/************************************************************************
*/
function tripal_analysis_go_org_charts ($element) {
$analysis_id = preg_replace("/^(\d+)-(\d+)$/","$1",$element);
$organism_id = preg_replace("/^(\d+)-(\d+)$/","$2",$element);
$content = '';
if($analysis_id and $organism_id){
$content = "
<b>Biological Process</b>
<br><i>Expand the tree to browse term counts. Click a term to view term details.</i>
<div class=\"tripal_cv_tree\" id=\"tripal_analysis_go_cv_tree_".$organism_id."-".$analysis_id."_bp\"></div>
<br><br><img class=\"tripal_cv_chart\" id=\"tripal_analysis_go_cv_chart_".$organism_id."-".$analysis_id."_bp\" src=\"\" border=\"0\">
<br><br><br><br>
<b>Cellular Component</b>
<br><i>Expand the tree to browse term counts. Click a term to view term details.</i>
<div class=\"tripal_cv_tree\" id=\"tripal_analysis_go_cv_tree_".$organism_id."-".$analysis_id."_cc\"></div>
<br><br><img class=\"tripal_cv_chart\" id=\"tripal_analysis_go_cv_chart_".$organism_id."-".$analysis_id."_cc\" src=\"\" border=\"0\">
<br><br><br><br>
<b>Molecular Function</b>
<br><i>Expand the tree to browse term counts. Click a term to view term details.</i>
<div class=\"tripal_cv_tree\" id=\"tripal_analysis_go_cv_tree_".$organism_id."-".$analysis_id."_mf\"></div>
<br><br><img class=\"tripal_cv_chart\" id=\"tripal_analysis_go_cv_chart_".$organism_id."-".$analysis_id."_mf\" src=\"\" border=\"0\">
";
}
$opt = array($content);
return drupal_json($opt);
}
/************************************************************************
*/
function tripal_analysis_go_load_organism_go_summary($node) {
$organism = $node->organism;
// check to see if we have any analyses
$sql = "
SELECT count(*) as cnt
FROM {go_count_analysis} GCA
INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id
WHERE organism_id = %d
";
$previous_db = tripal_db_set_active('chado');
$results = db_fetch_object(db_query($sql,$organism->organism_id));
tripal_db_set_active($previous_db);
$has_results = 0;
if($results->cnt > 0){
$has_results = 1;
}
return array (
'has_results' => $has_results,
'form' => drupal_get_form('tripal_analysis_go_select_form',$node),
);
}
/************************************************************************
*
*/
function tripal_analysis_go_cv_chart($chart_id){
// The CV module will create the JSON array necessary for buillding a
// pie chart using jgChart and Google Charts. We have to pass to it
// a table that contains count information, tell it which column
// contains the cvterm_id and provide a filter for getting the
// results we want from the table.
$organism_id = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$chart_id);
$analysis_id = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$chart_id);
$type = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$3",$chart_id);
$sql = "SELECT * FROM {Analysis} WHERE analysis_id = %d";
$previous_db = tripal_db_set_active('chado'); // use chado database
$analysis = db_fetch_object(db_query($sql,$analysis_id));
tripal_db_set_active($previous_db); // now use drupal database
if(strcmp($type,'mf')==0){
$class = 'molecular_function';
$title = "Number of Molecular Function Terms From $analysis->name Analysis";
}
if(strcmp($type,'cc')==0){
$class = 'cellular_component';
$title = "Number of Cellular Component Terms From $analysis->name Analysis";
}
if(strcmp($type,'bp')==0){
$class = 'biological_process';
$title = "Number of Biological Process Terms From $analysis->name Analysis";
}
$options = array(
count_mview => 'go_count_analysis',
cvterm_id_column => 'cvterm_id',
count_column => 'feature_count',
filter => "
CNT.organism_id = $organism_id AND
CNT.analysis_id = $analysis_id AND
CNT.cvterm_id IN (
SELECT CVTR.subject_id
FROM {CVTerm_relationship} CVTR
INNER JOIN CVTerm CVT on CVTR.object_id = CVT.cvterm_id
INNER JOIN CV on CVT.cv_id = CV.cv_id
WHERE CVT.name = '$class' AND
CV.name = '$class'
)
",
type => 'p',
size => '550x175',
title => $title,
);
return $options;
}
/************************************************************************
*
*/
function tripal_analysis_go_cv_tree($tree_id){
$organism_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$tree_id);
$analysis_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$tree_id);
$type = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$3",$tree_id);
if(strcmp($type,'mf')==0){
$class = 'molecular_function';
}
if(strcmp($type,'cc')==0){
$class = 'cellular_component';
}
if(strcmp($type,'bp')==0){
$class = 'biological_process';
}
$options = array(
cv_id => tripal_cv_get_cv_id($class),
count_mview => 'go_count_analysis',
cvterm_id_column => 'cvterm_id',
count_column => 'feature_count',
filter => "CNT.organism_id = $organism_id AND CNT.analysis_id = $analysis_id",
label => 'Features',
);
return $options;
}
/************************************************************************
*/
function tripal_analysis_go_cvterm_add($cvterm_id,$tree_id){
$organism_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$tree_id);
$analysis_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$tree_id);
$sql = "
SELECT DBX.accession
FROM {cvterm} CVT
INNER JOIN dbxref DBX on DBX.dbxref_id = CVT.dbxref_id
WHERE cvterm_id = %d
";
$previous_db = tripal_db_set_active('chado');
$xref = db_fetch_object(db_query($sql,$cvterm_id));
tripal_db_set_active($previous_db);
$link = url("download_goterm_features/$cvterm_id/$tree_id");
$options = array(
'Download sequences' => "<a href=\"$link\">GO_".$xref->accession.".fasta</a>",
);
return $options;
}
/************************************************************************
*/
function tripal_analysis_go_get_goterm_features($cvterm_id,$tree_id){
// get hte accession number for this cvterm and use it in naming the download
$sql = "
SELECT DBX.accession
FROM {cvterm} CVT
INNER JOIN dbxref DBX on DBX.dbxref_id = CVT.dbxref_id
WHERE cvterm_id = %d
";
$previous_db = tripal_db_set_active('chado');
$xref = db_fetch_object(db_query($sql,$cvterm_id));
tripal_db_set_active($previous_db);
drupal_set_header('Content-Type: text');
drupal_set_header('Content-Disposition: attachment; filename="GO_'.$xref->accession.'.fasta"');
$organism_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$tree_id);
$analysis_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$tree_id);
$sql = "
SELECT DISTINCT F.name,F.residues,F.feature_id
FROM {cvtermpath} CVTP
INNER JOIN CVTerm CVT1 on CVTP.subject_id = CVT1.cvterm_id
INNER JOIN CVTerm CVT2 on CVTP.object_id = CVT2.cvterm_id
INNER JOIN AnalysisFeatureProp AFP on AFP.type_id = CVTP.subject_id
INNER JOIN AnalysisFeature AF on AF.analysisfeature_id = AFP.analysisfeature_id
INNER JOIN Feature F on AF.feature_id = F.feature_id
WHERE CVTP.object_id = %d and F.organism_id = %d and AF.analysis_id = %d
ORDER BY F.name
";
$previous_db = tripal_db_set_active('chado');
$results = db_query($sql,$cvterm_id,$organism_id,$analysis_id);
tripal_db_set_active($previous_db);
while($feature = db_fetch_object($results)){
// get the go term information for each sequence
$sql = "
SELECT CVT.name,DBX.accession
FROM {Feature_CVTerm} FCVT
INNER JOIN CVTerm CVT on FCVT.cvterm_id = CVT.cvterm_id
INNER JOIN DBXref DBX on CVT.dbxref_id = DBX.dbxref_id
WHERE FCVT.feature_id = %d
";
$previous_db = tripal_db_set_active('chado');
$terms = db_query($sql,$feature->feature_id);
tripal_db_set_active($previous_db);
$desc = '[';
while($term = db_fetch_object($terms)){
$desc .= "GO:$term->accession $term->name; ";
}
$desc = chop($desc);
$desc = chop($desc,';');
$desc .= ']';
print tripal_feature_return_fasta($feature, $desc);
}
return;
}
/************************************************************************
*/
function tripal_analysis_go_load_feature_terms($feature) {
$sql = "
SELECT DISTINCT FCVT.feature_id,DBX.accession,CVT.name as goterm,
CVT.cvterm_id as go_id, CV.name as cvname, CVT.definition
FROM {Feature_Cvterm} FCVT
INNER JOIN Cvterm CVT ON CVT.cvterm_ID = FCVT.cvterm_ID
INNER JOIN CV ON CV.cv_id = CVT.cv_id
INNER JOIN dbxref DBX ON DBX.dbxref_id = CVT.dbxref_id
WHERE
(CV.name = 'biological_process' OR
CV.name = 'cellular_component' OR
CV.name = 'molecular_function') AND
FCVT.feature_id = %d
ORDER BY CV.name, CVT.name
";
$previous_db = tripal_db_set_active('chado');
$results = db_query($sql,$feature->feature_id);
tripal_db_set_active($previous_db);
$i=0;
$terms = array();
while($term = db_fetch_object($results)){
$terms[$i++] = $term;
}
return $terms;
}
/*******************************************************************************
* Tripal GO administrative setting form. This function is called by
* tripal_analysis module which asks for an admin form to show on the page
*/
function tripal_analysis_go_get_settings() {
// Get an array of node types with internal names as keys
$options = node_get_types('names');
// Add 'chado_feature' to allowed content types for showing unigene results
$allowedoptions ['chado_feature'] = "Show GO terms on feature pages";
$allowedoptions ['chado_organism'] = "Show GO analysis on organism pages";
$form['description'] = array(
'#type' => 'item',
'#value' => t("This option allows user to display the Gene Ontology (GO) ".
"information. For features, this would include all GO terms assigned to a feature ".
"and for organisms this would be statistical pie charts of GO terms for a organism. Check the box to ".
"enable the display of GO information. Uncheck to disable."),
'#weight' => 0,
);
$form['tripal_analysis_go_setting'] = array(
'#type' => 'checkboxes',
'#options' => $allowedoptions,
'#default_value'=>variable_get('tripal_analysis_go_setting',array('chado_feature', 'chado_organism')),
);
$settings->form = $form;
$settings->title = "Tripal GO";
return $settings;
}
/**
*
*
* @ingroup tripal_feature
*/
function tripal_analysis_go_job_describe_args($callback,$args){
$new_args = array();
if($callback == 'tripal_analysis_go_load_gaf'){
$new_args['GAF 2.0 file'] = $args[0];
$organism = tripal_core_chado_select('organism',array('genus','species'),array('organism_id' => $args[1]));
$new_args['Organism'] = $organism[0]->genus." ". $organism[0]->species;
$new_args['Sequence Type'] = $args[8];
// add in the analysis
if($args[2]){
$analysis = tripal_core_chado_select('analysis',array('name'),array('analysis_id' => $args[2]));
}
$new_args['Analysis'] = $analysis[0]->name;
if($args[3]){
$new_args['Function to perform'] = 'Add GO terms';
}
if($args[4]){
$new_args['Function to perform'] = 'Replace GO terms';
}
if($args[5]){
$new_args['Function to perform'] = 'Delete GO terms';
}
$new_args['Regular expression for the feature name'] = $args[6];
$new_args['Regular expression for the feature unique name'] = $args[7];
}
return $new_args;
}