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Tripal v1.0 (6.x-1.0)
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Tripal v1.0 (6.x-1.0)
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Functions | |
| tripal_feature_gff3_load_form () | |
| tripal_feature_gff3_load_form_validate ($form, &$form_state) | |
| tripal_feature_gff3_load_form_submit ($form, &$form_state) | |
| tripal_feature_load_gff3 ($gff_file, $organism_id, $analysis_id, $add_only=0, $update=0, $refresh=0, $remove=0, $use_transaction=1, $target_organism_id=NULL, $target_type=NULL, $create_target=0, $start_line=1, $landmark_type= '', $alt_id_attr= '', $job=NULL) | |
| tripal_feature_load_gff3_derives_from ($feature, $subject, $organism) | |
| tripal_feature_load_gff3_parents ($feature, $cvterm, $parents, $organism_id, $fmin) | |
| tripal_feature_load_gff3_dbxref ($feature, $dbxrefs) | |
| tripal_feature_load_gff3_ontology ($feature, $dbxrefs) | |
| tripal_feature_load_gff3_alias ($feature, $aliases) | |
| tripal_feature_load_gff3_feature ($organism, $analysis_id, $cvterm, $uniquename, $name, $residues, $is_analysis= 'f', $is_obsolete= 'f', $add_only, $score) | |
| tripal_feature_load_gff3_featureloc ($feature, $organism, $landmark, $fmin, $fmax, $strand, $phase, $is_fmin_partial, $is_fmax_partial, $residue_info, $locgroup, $landmark_type_id= '', $landmark_organism_id= '', $create_landmark=0, $landmark_is_target=0) | |
| tripal_feature_load_gff3_property ($feature, $property, $value) | |
Provides gff3 loading functionality. Creates features based on their specification in a GFF3 file.
| tripal_feature_gff3_load_form | ( | ) |
Definition at line 21 of file gff_loader.inc.
{
$form['gff_file']= array(
'#type' => 'textfield',
'#title' => t('GFF3 File'),
'#description' => t('Please enter the full system path for the GFF file, or a path within the Drupal
installation (e.g. /sites/default/files/xyz.gff). The path must be accessible to the
server on which this Drupal instance is running.'),
'#required' => TRUE,
);
// get the list of organisms
$sql = "SELECT * FROM {organism} ORDER BY genus, species";
$org_rset = chado_query($sql);
$organisms = array();
$organisms[''] = '';
while ($organism = db_fetch_object($org_rset)) {
$organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
}
$form['organism_id'] = array(
'#title' => t('Organism'),
'#type' => t('select'),
'#description' => t("Choose the organism to which these sequences are associated"),
'#required' => TRUE,
'#options' => $organisms,
);
// get the list of analyses
$sql = "SELECT * FROM {analysis} ORDER BY name";
$org_rset = chado_query($sql);
$analyses = array();
$analyses[''] = '';
while ($analysis = db_fetch_object($org_rset)) {
$analyses[$analysis->analysis_id] = "$analysis->name ($analysis->program $analysis->programversion, $analysis->sourcename)";
}
$form['analysis_id'] = array(
'#title' => t('Analysis'),
'#type' => t('select'),
'#description' => t("Choose the analysis to which these features are associated.
Why specify an analysis for a data load? All data comes
from some place, even if downloaded from Genbank. By specifying
analysis details for all data imports it allows an end user to reproduce the
data set, but at least indicates the source of the data."),
'#required' => TRUE,
'#options' => $analyses,
);
$form['line_number']= array(
'#type' => 'textfield',
'#title' => t('Start Line Number'),
'#description' => t('Enter the line number in the GFF file where you would like to begin processing. The
first line is line number 1. This option is useful for examining loading problems with large GFF files.'),
'#size' => 10,
);
$form['landmark_type'] = array(
'#title' => t('Landmark Type'),
'#type' => t('textfield'),
'#description' => t("Optional. Use this field to specify a Sequence Ontology type
for the landmark sequences in the GFF fie (e.g. 'chromosome'). If the GFF file
contains a '##sequence-region' line that describes the landmark sequences to
which all others are aligned and a type is provided here then the features
will be created if they do not already exist. If they do exist then this
field is not used."),
);
$form['alt_id_attr'] = array(
'#title' => t('ID Attribute'),
'#type' => t('textfield'),
'#description' => t("Optional. Sometimes lines in the GFF file are missing the
required ID attribute that specifies the unique name of the feature. If so,
you may specify an the name of an existing attribute to use for the name."),
);
$form['import_options'] = array(
'#type' => 'fieldset',
'#title' => t('Import Options'),
'#collapsed' => TRUE
);
$form['import_options']['use_transaction']= array(
'#type' => 'checkbox',
'#title' => t('Use a transaction'),
'#required' => FALSE,
'#description' => t('Use a database transaction when loading the GFF file. If an error occurs
the entire datset loaded prior to the failure will be rolled back and will not be available
in the database. If this option is unchecked and failure occurs all records up to the point
of failure will be present in the database.'),
'#default_value' => 1,
);
$form['import_options']['add_only']= array(
'#type' => 'checkbox',
'#title' => t('Import only new features'),
'#required' => FALSE,
'#description' => t('The job will skip features in the GFF file that already
exist in the database and import only new features.'),
);
$form['import_options']['update']= array(
'#type' => 'checkbox',
'#title' => t('Import all and update'),
'#required' => FALSE,
'#default_value' => 'checked',
'#description' => t('Existing features will be updated and new features will be added. Attributes
for a feature that are not present in the GFF but which are present in the
database will not be altered.'),
);
$form['import_options']['refresh']= array(
'#type' => 'checkbox',
'#title' => t('Import all and replace'),
'#required' => FALSE,
'#description' => t('Existing features will be updated and feature properties not
present in the GFF file will be removed.'),
);
$form['import_options']['remove']= array(
'#type' => 'checkbox',
'#title' => t('Delete features'),
'#required' => FALSE,
'#description' => t('Features present in the GFF file that exist in the database
will be removed rather than imported'),
);
$form['targets'] = array(
'#type' => 'fieldset',
'#title' => t('Targets'),
'#collapsed' => TRUE
);
$form['targets']['adesc'] = array(
'#type' => 'markup',
'#value' => t("When alignments are represented in the GFF file (e.g. such as
alignments of cDNA sequences to a whole genome, or blast matches), they are
represented using two feature types: 'match' (or cDNA_match, EST_match, etc.)
and 'match_part'. These features may also have a 'Target' attribute to
specify the sequence that is being aligned.
However, the organism to which the aligned sequence belongs may not be present in the
GFF file. Here you can specify the organism and feature type of the target sequences.
The options here will apply to all targets unless the organism and type are explicity
set in the GFF file using the 'target_organism' and 'target_type' attributes."),
);
$form['targets']['target_organism_id'] = array(
'#title' => t('Target Organism'),
'#type' => t('select'),
'#description' => t("Optional. Choose the organism to which target sequences belong.
Select this only if target sequences belong to a different organism than the
one specified above. And only choose an organism here if all of the target sequences
belong to the same species. If the targets in the GFF file belong to multiple
different species then the organism must be specified using the 'target_organism=genus:species'
attribute in the GFF file."),
'#options' => $organisms,
);
$form['targets']['target_type'] = array(
'#title' => t('Target Type'),
'#type' => t('textfield'),
'#description' => t("Optional. If the unique name for a target sequence is not unique (e.g. a protein
and an mRNA have the same name) then you must specify the type for all targets in the GFF file. If
the targets are of different types then the type must be specified using the 'target_type=type' attribute
in the GFF file. This must be a valid Sequence Ontology (SO) term."),
);
$form['targets']['create_target']= array(
'#type' => 'checkbox',
'#title' => t('Create Target'),
'#required' => FALSE,
'#description' => t("If the target feature cannot be found, create one using the organism and type specified above, or
using the 'target_organism' and 'target_type' fields specified in the GFF file. Values specified in the
GFF file take precedence over those specified above."),
);
$form['button'] = array(
'#type' => 'submit',
'#value' => t('Import GFF3 file'),
'#weight' => 10,
);
return $form;
}
| tripal_feature_gff3_load_form_submit | ( | $ | form, |
| &$ | form_state | ||
| ) |
Definition at line 247 of file gff_loader.inc.
{
global $user;
$gff_file = trim($form_state['values']['gff_file']);
$organism_id = $form_state['values']['organism_id'];
$add_only = $form_state['values']['add_only'];
$update = $form_state['values']['update'];
$refresh = $form_state['values']['refresh'];
$remove = $form_state['values']['remove'];
$analysis_id = $form_state['values']['analysis_id'];
$use_transaction = $form_state['values']['use_transaction'];
$target_organism_id = $form_state['values']['target_organism_id'];
$target_type = trim($form_state['values']['target_type']);
$create_target = $form_state['values']['create_target'];
$line_number = trim($form_state['values']['line_number']);
$landmark_type = trim($form_state['values']['landmark_type']);
$alt_id_attr = trim($form_state['values']['alt_id_attr']);
$args = array($gff_file, $organism_id, $analysis_id, $add_only,
$update, $refresh, $remove, $use_transaction, $target_organism_id,
$target_type, $create_target, $line_number, $landmark_type, $alt_id_attr);
$type = '';
if ($add_only) {
$type = 'import only new features';
}
if ($update) {
$type = 'import all and update';
}
if ($refresh) {
$type = 'import all and replace';
}
if ($remove) {
$type = 'delete features';
}
$fname = preg_replace("/.*\/(.*)/", "$1", $gff_file);
tripal_add_job("$type GFF3 file: $fname", 'tripal_feature',
'tripal_feature_load_gff3', $args, $user->uid);
return '';
}
| tripal_feature_gff3_load_form_validate | ( | $ | form, |
| &$ | form_state | ||
| ) |
Definition at line 200 of file gff_loader.inc.
{
$gff_file = trim($form_state['values']['gff_file']);
$organism_id = $form_state['values']['organism_id'];
$target_organism_id = $form_state['values']['target_organism_id'];
$target_type = trim($form_state['values']['target_type']);
$create_target = $form_state['values']['create_target'];
$add_only = $form_state['values']['add_only'];
$update = $form_state['values']['update'];
$refresh = $form_state['values']['refresh'];
$remove = $form_state['values']['remove'];
$use_transaction = $form_state['values']['use_transaction'];
$line_number = trim($form_state['values']['line_number']);
$landmark_type = trim($form_state['values']['landmark_type']);
$alt_id_attr = trim($form_state['values']['alt_id_attr']);
// check to see if the file is located local to Drupal
$gff_file = trim($gff_file);
$dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $gff_file;
if (!file_exists($dfile)) {
// if not local to Drupal, the file must be someplace else, just use
// the full path provided
$dfile = $gff_file;
}
if (!file_exists($dfile)) {
form_set_error('gff_file', t("Cannot find the file on the system. Check that the file exists or that the web server has permissions to read the file."));
}
// @coder-ignore: there are no functions being called here
if (($add_only AND ($update OR $refresh OR $remove)) OR
($update AND ($add_only OR $refresh OR $remove)) OR
($refresh AND ($update OR $add_only OR $remove)) OR
($remove AND ($update OR $refresh OR $add_only))) {
form_set_error('add_only', t("Please select only one checkbox from the import options section"));
}
if ($line_number and !is_numeric($line_number) or $line_number < 0) {
form_set_error('line_number', t("Please provide an integer line number greater than zero."));
}
}
| tripal_feature_load_gff3 | ( | $ | gff_file, |
| $ | organism_id, | ||
| $ | analysis_id, | ||
| $ | add_only = 0, |
||
| $ | update = 0, |
||
| $ | refresh = 0, |
||
| $ | remove = 0, |
||
| $ | use_transaction = 1, |
||
| $ | target_organism_id = NULL, |
||
| $ | target_type = NULL, |
||
| $ | create_target = 0, |
||
| $ | start_line = 1, |
||
| $ | landmark_type = '', |
||
| $ | alt_id_attr = '', |
||
| $ | job = NULL |
||
| ) |
Definition at line 294 of file gff_loader.inc.
{
// make sure our temporary table exists
$ret = array();
if (!db_table_exists('tripal_gff_temp')) {
$schema = tripal_feature_get_custom_tables('tripal_gff_temp');
$success = tripal_core_create_custom_table($ret, 'tripal_gff_temp', $schema['tripal_gff_temp']);
if (!$success) {
watchdog('T_gff3_loader', "Cannot create temporary loading table", array(), WATCHDOG_ERROR);
return;
}
}
// empty the temp table
$sql = "DELETE FROM tripal_gff_temp";
chado_query($sql);
// get a persistent connection
$connection = tripal_db_persistent_chado();
if (!$connection) {
print "A persistant connection was not obtained. Loading will be slow\n";
}
// begin the transaction
if ($use_transaction) {
tripal_db_start_transaction();
// if we cannot get a connection then let the user know the loading will be slow
if (!$connection) {
print "A persistant connection was not obtained. Loading will be slow\n";
}
else {
print "\nNOTE: Loading of this GFF file is performed using a database transaction. \n" .
"If the load fails or is terminated prematurely then the entire set of \n" .
"insertions/updates is rolled back and will not be found in the database\n\n";
}
}
// check to see if the file is located local to Drupal
$dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $gff_file;
if (!file_exists($dfile)) {
// if not local to Drupal, the file must be someplace else, just use
// the full path provided
$dfile = $gff_file;
}
if (!file_exists($dfile)) {
watchdog('T_gff3_loader', "Cannot find the file: %dfile",
array('%dfile' => $dfile), WATCHDOG_ERROR);
return 0;
}
print "Opening $gff_file\n";
//$lines = file($dfile,FILE_SKIP_EMPTY_LINES);
$fh = fopen($dfile, 'r');
if (!$fh) {
watchdog('T_gff3_loader', "cannot open file: %dfile",
array('%dfile' => $dfile), WATCHDOG_ERROR);
return 0;
}
$filesize = filesize($dfile);
// get the controlled vocaubulary that we'll be using. The
// default is the 'sequence' ontology
// @coder-ignore: non-drupal schema thus table prefixing does not apply
$sql = "SELECT * FROM cv WHERE name = '%s'";
$cv = db_fetch_object(chado_query($sql, 'sequence'));
if (!$cv) {
watchdog('T_gff3_loader', "Cannot find the 'sequence' ontology",
array(), WATCHDOG_ERROR);
return '';
}
// get the organism for which this GFF3 file belongs
// @coder-ignore: non-drupal schema thus table prefixing does not apply
$sql = "SELECT * FROM organism WHERE organism_id = %d";
$organism = db_fetch_object(chado_query($sql, $organism_id));
$interval = intval($filesize * 0.0001);
if ($interval == 0) {
$interval = 1;
}
$in_fasta = 0;
$line_num = 0;
$num_read = 0;
$intv_read = 0;
// prepare the statement used to get the cvterm for each feature.
if (!tripal_core_is_sql_prepared('sel_cvterm_idnasy')) {
$psql = "PREPARE sel_cvterm_idnasy (int, text, text) AS
SELECT CVT.cvterm_id, CVT.cv_id, CVT.name, CVT.definition,
CVT.dbxref_id, CVT.is_obsolete, CVT.is_relationshiptype
FROM {cvterm} CVT
INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
WHERE CV.cv_id = $1 and
(lower(CVT.name) = lower($2) or lower(CVTS.synonym) = lower($3))";
$status = tripal_core_chado_prepare('sel_cvterm_idnasy', $psql, array('int','text','text'));
if (!$status) {
watchdog('T_gff3_loader', 'cannot prepare statement \'sel_cvterm_idnasy\'.',
array(), WATCHDOG_ERROR);
return '';
}
}
// iterate through each line of the GFF file
print "Parsing Line $line_num (0.00%). Memory: " . number_format(memory_get_usage()) . " bytes\r";
while ($line = fgets($fh)) {
$line_num++;
$size = drupal_strlen($line);
$num_read += $size;
$intv_read += $size;
if($line_num < $start_line) {
continue;
}
// update the job status every 1% features
if ($job and $intv_read >= $interval) {
$intv_read = 0;
$percent = sprintf("%.2f", ($num_read / $filesize) * 100);
print "Parsing Line $line_num (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
tripal_job_set_progress($job, intval(($num_read / $filesize) * 100));
}
// check to see if we have FASTA section, if so then set the variable
// to start parsing
if (preg_match('/^##FASTA/i', $line)) {
if($remove) {
// we're done because this is a delete operation so break out of the loop.
break;
}
tripal_feature_load_gff3_fasta($fh, $interval, $num_read, $intv_read, $line_num);
continue;
}
// if the ##sequence-region line is present then we want to add a new feature
if (preg_match('/^##sequence-region (.*?) (\d+) (\d+)$/i', $line, $region_matches)) {
$rid = $region_matches[1];
$rstart = $region_matches[2];
$rend = $region_matches[3];
if ($landmark_type) {
$result = chado_query("EXECUTE sel_cvterm_idnasy (%d, '%s', '%s')", $cv->cv_id, $landmark_type, $landmark_type);
$cvterm = db_fetch_object($result);
if (!$cvterm) {
watchdog('T_gff3_loader', 'cannot find feature term \'%landmark_type\' on line %line_num of the GFF file',
array('%landmark_type' => $landmark_type, '%line_num' => $line_num), WATCHDOG_ERROR);
return '';
}
tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $rid,
$rid, '', 'f', 'f', 1, 0);
}
continue;
}
// skip comments
if (preg_match('/^#/', $line)) {
continue;
}
// skip empty lines
if (preg_match('/^\s*$/', $line)) {
continue;
}
// get the columns
$cols = explode("\t", $line);
if (sizeof($cols) != 9) {
watchdog('T_gff3_loader', 'improper number of columns on line %line_num',
array('%line_num' => $line_num), WATCHDOG_ERROR);
return '';
}
// get the column values
$landmark = $cols[0];
$source = $cols[1];
$type = $cols[2];
$start = $cols[3];
$end = $cols[4];
$score = $cols[5];
$strand = $cols[6];
$phase = $cols[7];
$attrs = explode(";", $cols[8]); // split by a semicolon
// ready the start and stop for chado. Chado expects these positions
// to be zero-based, so we substract 1 from the fmin
$fmin = $start - 1;
$fmax = $end;
if ($end < $start) {
$fmin = $end - 1;
$fmax = $start;
}
// format the strand for chado
if (strcmp($strand, '.') == 0) {
$strand = 0;
}
elseif (strcmp($strand, '+') == 0) {
$strand = 1;
}
elseif (strcmp($strand, '-') == 0) {
$strand = -1;
}
if (strcmp($phase, '.') == 0) {
$phase = '';
}
$result = chado_query("EXECUTE sel_cvterm_idnasy (%d, '%s', '%s')", $cv->cv_id, $type, $type);
$cvterm = db_fetch_object($result);
if (!$cvterm) {
watchdog('T_gff3_loader', 'cannot find feature term \'%type\' on line %line_num of the GFF file',
array('%type' => $type, '%line_num' => $line_num), WATCHDOG_ERROR);
return '';
}
// break apart each of the attributes
$tags = array();
$attr_name = '';
$attr_uniquename = '';
$attr_residue_info = '';
$attr_locgroup = 0;
$attr_fmin_partial = 'f';
$attr_fmax_partial = 'f';
$attr_is_obsolete = 'f';
$attr_is_analysis = 'f';
$attr_others = '';
$residues = '';
foreach ($attrs as $attr) {
$attr = rtrim($attr);
$attr = ltrim($attr);
if (strcmp($attr, '')==0) {
continue;
}
if (!preg_match('/^[^\=]+\=.+$/', $attr)) {
watchdog('T_gff3_loader', 'Attribute is not correctly formatted on line %line_num: %attr',
array('%line_num' => $line_num, '%attr' => $attr), WATCHDOG_ERROR);
return '';
}
// break apart each tag
$tag = preg_split("/=/", $attr, 2); // split by equals sign
// multiple instances of an attribute are separated by commas
$tag_name = $tag[0];
if (!array_key_exists($tag_name, $tags)) {
$tags[$tag_name] = array();
}
$tags[$tag_name] = array_merge($tags[$tag_name], explode(",", $tag[1])); // split by comma
// replace the URL escape codes for each tag
for ($i = 0; $i < count($tags[$tag_name]); $i++) {
$tags[$tag_name][$i] = urldecode($tags[$tag_name][$i]);
}
// get the name and ID tags
if (strcmp($tag_name, 'ID') == 0) {
$attr_uniquename = urldecode($tag[1]);
}
elseif (strcmp($tag_name, 'Name') == 0) {
$attr_name = urldecode($tag[1]);
}
// get the list of non-reserved attributes
elseif (strcmp($tag_name, 'Alias') !=0 and strcmp($tag_name, 'Parent') !=0 and
strcmp($tag_name, 'Target') !=0 and strcmp($tag_name, 'Gap') !=0 and
strcmp($tag_name, 'Derives_from') !=0 and strcmp($tag_name, 'Note') !=0 and
strcmp($tag_name, 'Dbxref') !=0 and strcmp($tag_name, 'Ontology_term') !=0 and
strcmp($tag_name, 'Is_circular') !=0 and strcmp($tag_name, 'target_organism') !=0 and
strcmp($tag_name, 'target_type') != 0) {
foreach ($tags[$tag_name] as $value) {
$attr_others[$tag_name][] = $value;
}
}
}
// if neither name nor uniquename are provided then generate one
if (!$attr_uniquename and !$attr_name) {
// check if an alternate ID field is suggested, if so, then use
// that for the name
if (array_key_exists($alt_id_attr, $tags)) {
$attr_uniquename = $tags[$alt_id_attr][0];
$attr_name = $attr_uniquename;
}
// if the row has a parent then generate a uniquename using the parent name
elseif (array_key_exists('Parent', $tags)) {
$attr_uniquename = $tags['Parent'][0] . "-$type-$landmark:$fmin..$fmax";
$attr_name = $attr_uniquename;
}
// generate a unique name based on the date, type and location
// and set the name to simply be the type
else {
$date = getdate();
$attr_uniquename = $date[0] . "-$type-$landmark:$fmin..$fmax";
$attr_name = $type;
}
}
// if a name is not specified then use the unique name
if (strcmp($attr_name, '')==0) {
$attr_name = $attr_uniquename;
}
// if an ID attribute is not specified then use the attribute name and
// hope for the best
if (!$attr_uniquename) {
$attr_uniquename = $attr_name;
}
// make sure the landmark sequence exists in the database. We don't
// know the type of the landmark so we'll hope that it's unique across
// all types. If not we'll error out. This test is only necessary if
// if the landmark and the uniquename are different. If they are the same
// then this is the information for the landmark
if (!$remove and strcmp($landmark, $attr_uniquename) != 0 ) {
$select = array(
'organism_id' => $organism_id,
'uniquename' => $landmark,
);
$columns = array('count(*) as num_landmarks');
$options = array('statement_name' => 'sel_feature_numland');
$count = tripal_core_chado_select('feature', $columns, $select, $options);
if (!$count or count($count) == 0 or $count[0]->num_landmarks == 0) {
watchdog('T_gff3_loader', "The landmark '%landmark' cannot be found for this organism (" . $organism->genus . " " . $organism->species . ") " .
"Please add the landmark and then retry the import of this GFF3 ".
"file", array('%landmark' => $landmark), WATCHDOG_ERROR);
return '';
}
if ($count[0]->num_landmarks > 1) {
watchdog('T_gff3_loader', "The landmark '%landmark' is not unique for this organism. ".
"The features cannot be associated", array('%landmark' => $landmark), WATCHDOG_ERROR);
return '';
}
}
// if the option is to remove or refresh then we want to remove
// the feature from the database.
if ($remove or $refresh) {
$sql = "DELETE FROM {feature}
WHERE organism_id = %d and uniquename = '%s' and type_id = %d";
$match = array(
'organism_id' => $organism->organism_id,
'uniquename' => $attr_uniquename,
'type_id' => $cvterm->cvterm_id
);
$result = tripal_core_chado_delete('feature', $match);
if (!$result) {
watchdog('T_gff3_loader', "cannot delete feature %attr_uniquename",
array('%attr_uniquename' => $attr_uniquename), WATCHDOG_ERROR);
}
$feature = 0;
unset($result);
}
// add or update the feature and all properties
if ($update or $refresh or $add_only) {
// add/update the feature
$feature = tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm,
$attr_uniquename, $attr_name, $residues, $attr_is_analysis,
$attr_is_obsolete, $add_only, $score);
if ($feature) {
// add a record for this feature to the tripal_gff_temp table for
// later lookup
$values = array(
'feature_id' => $feature->feature_id,
'organism_id' => $feature->organism_id,
'type_name' => $type,
'uniquename' => $feature->uniquename
);
// make sure this record doesn't already exist in oru temp table
$options = array('statement_name' => 'sel_tripalgfftemp_all');
$results = tripal_core_chado_select('tripal_gff_temp', array('*'), $values, $options);
if (count($results) == 0) {
$options = array('statement_name' => 'ins_tripalgfftemp');
$result = tripal_core_chado_insert('tripal_gff_temp', $values, $options);
if (!$result) {
watchdog('T_gff3_loader', "Cound not save record in temporary table, Cannot continue.", array(), WATCHDOG_ERROR);
exit;
}
}
// add/update the featureloc if the landmark and the ID are not the same
// if they are the same then this entry in the GFF is probably a landmark identifier
if (strcmp($landmark, $attr_uniquename) !=0 ) {
tripal_feature_load_gff3_featureloc($feature, $organism,
$landmark, $fmin, $fmax, $strand, $phase, $attr_fmin_partial,
$attr_fmax_partial, $attr_residue_info, $attr_locgroup);
}
// add any aliases for this feature
if (array_key_exists('Alias', $tags)) {
tripal_feature_load_gff3_alias($feature, $tags['Alias']);
}
// add any dbxrefs for this feature
if (array_key_exists('Dbxref', $tags)) {
tripal_feature_load_gff3_dbxref($feature, $tags['Dbxref']);
}
// add any ontology terms for this feature
if (array_key_exists('Ontology_term', $tags)) {
tripal_feature_load_gff3_ontology($feature, $tags['Ontology_term']);
}
// add parent relationships
if (array_key_exists('Parent', $tags)) {
tripal_feature_load_gff3_parents($feature, $cvterm, $tags['Parent'], $organism_id, $fmin);
}
// add target relationships
if (array_key_exists('Target', $tags)) {
tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $target_type, $create_target, $attr_locgroup);
}
// add gap information. This goes in simply as a property
if (array_key_exists('Gap', $tags)) {
foreach ($tags['Gap'] as $value) {
tripal_feature_load_gff3_property($feature, 'Gap', $value);
}
}
// add notes. This goes in simply as a property
if (array_key_exists('Note', $tags)) {
foreach ($tags['Note'] as $value) {
tripal_feature_load_gff3_property($feature, 'Note', $value);
}
}
// add the Derives_from relationship (e.g. polycistronic genes).
if (array_key_exists('Derives_from', $tags)) {
tripal_feature_load_gff3_derives_from($feature, $tags['Derives_from'][0], $organism);
}
// add in the GFF3_source dbxref so that GBrowse can find the feature using the source column
$source_ref = array('GFF_source:' . $source);
tripal_feature_load_gff3_dbxref($feature, $source_ref);
// add any additional attributes
if ($attr_others) {
foreach ($attr_others as $tag_name => $values) {
foreach ($values as $value) {
tripal_feature_load_gff3_property($feature, $tag_name, $value);
}
}
}
}
}
}
if (!$remove) {
print "\nSetting ranks of children...\n";
// get features in a relationship that are also children of an alignment
$sql = "SELECT DISTINCT F.feature_id, F.organism_id, F.type_id,
F.uniquename, FL.strand
FROM tripal_gff_temp TGT
INNER JOIN feature F ON TGT.feature_id = F.feature_id
INNER JOIN feature_relationship FR ON FR.object_id = TGT.feature_id
INNER JOIN cvterm CVT ON CVT.cvterm_id = FR.type_id
INNER JOIN featureloc FL ON FL.feature_id = F.feature_id
WHERE CVT.name = 'part_of'";
$parents = chado_query($sql);
// build and prepare the SQL for selecting the children relationship
$sql = "SELECT DISTINCT FR.feature_relationship_id, FL.fmin, FR.rank
FROM feature_relationship FR
INNER JOIN featureloc FL on FL.feature_id = FR.subject_id";
if (!$connection) {
$sql .= "WHERE FR.object_id = %d ".
"ORDER BY FL.fmin ASC ";
}
else {
$sql = "PREPARE sel_gffchildren (int) AS " . $sql . " WHERE FR.object_id = \$1 ORDER BY FL.fmin ASC";
}
if (!tripal_core_is_sql_prepared('sel_gffchildren')) {
$success = tripal_core_chado_prepare('sel_gffchildren', $sql, array('int'));
if (!$success) {
watchdog("T_gff3_loader", "Cannot prepare statement 'sel_gffchildren' and cannot set children ranks.",
array(), WATCHDOG_WARNING);
return 0;
}
}
// now set the rank of any parent/child relationships. The order is based
// on the fmin. The start rank is 1. This allows features with other
// relationships to be '0' (the default), and doesn't interfer with the
// ordering defined here.
while ($parent = db_fetch_object($parents)) {
// get the children
if ($connection) {
$result = chado_query('EXECUTE sel_gffchildren (%d)', $parent->feature_id);
}
else {
$result = chado_query($sql, $parent->feature_id);
}
// build an array of the children
$children = array();
while ($child = db_fetch_object($result)) {
$children[] = $child;
}
// the children list comes sorted in ascending fmin
// but if the parent is on the reverse strand we need to
// reverse the order of the children.
if ($parent->strand == -1) {
arsort($children);
}
// first set the ranks to a negative number so that we don't
// get a duplicate error message when we try to change any of them
$rank = -1;
foreach ($children as $child) {
$match = array('feature_relationship_id' => $child->feature_relationship_id);
$options = array('statement_name' => 'upd_featurerelationship_rank');
$values = array('rank' => $rank);
tripal_core_chado_update('feature_relationship', $match, $values, $options);
$rank--;
}
// now set the rank correctly. The rank should start at 0.
$rank = 0;
foreach ($children as $child) {
$match = array('feature_relationship_id' => $child->feature_relationship_id);
$options = array('statement_name' => 'upd_featurerelationship_rank');
$values = array('rank' => $rank);
//print "Was: " . $child->rank . " now $rank ($parent->strand)\n" ;
tripal_core_chado_update('feature_relationship', $match, $values, $options);
$rank++;
}
}
}
// commit the transaction
if ($use_transaction) {
tripal_db_commit_transaction();
}
print "Done\n";
return 1;
}
| tripal_feature_load_gff3_alias | ( | $ | feature, |
| $ | aliases | ||
| ) |
Definition at line 1173 of file gff_loader.inc.
{
// make sure we have a 'synonym_type' vocabulary
$select = array('name' => 'synonym_type');
$options = array('statement_name' => 'sel_cv_name');
$results = tripal_core_chado_select('cv', array('*'), $select, $options);
if (count($results) == 0) {
// insert the 'synonym_type' vocabulary
$values = array(
'name' => 'synonym_type',
'definition' => 'vocabulary for synonym types',
);
$options = array('statement_name' => 'ins_cv_name_definition');
$success = tripal_core_chado_insert('cv', $values, $options);
if (!$success) {
watchdog("T_gff3_loader", "Failed to add the synonyms type vocabulary", array(), WATCHDOG_WARNING);
return 0;
}
// now that we've added the cv we need to get the record
$options = array('statement_name' => 'sel_cv_name');
$results = tripal_core_chado_select('cv', array('*'), $select, $options);
if (count($results) > 0) {
$syncv = $results[0];
}
}
else {
$syncv = $results[0];
}
// get the 'exact' cvterm, which is the type of synonym we're adding
$select = array(
'name' => 'exact',
'cv_id' => array(
'name' => 'synonym_type'
),
);
$options = array('statement_name' => 'sel_cvterm_name_cvid');
$result = tripal_core_chado_select('cvterm', array('*'), $select, $options);
if (count($result) == 0) {
$term = array(
'name' => 'exact',
'id' => "internal:exact",
'definition' => '',
'is_obsolete' => 0,
);
// TODO: fix the function so it uses prepared statements
$syntype = tripal_cv_add_cvterm($term, $syncv->name, 0, 1);
if (!$syntype) {
watchdog("T_gff3_loader", "Cannot add synonym type: internal:$type", array(), WATCHDOG_WARNING);
return 0;
}
}
else {
$syntype = $result[0];
}
// iterate through all of the aliases and add each one
foreach ($aliases as $alias) {
// check to see if the alias already exists in the synonym table
// if not, then add it
$select = array(
'name' => $alias,
'type_id' => $syntype->cvterm_id,
);
$options = array('statement_name' => 'sel_synonym_name_typeid');
$result = tripal_core_chado_select('synonym', array('*'), $select, $options);
if (count($result) == 0) {
$values = array(
'name' => $alias,
'type_id' => $syntype->cvterm_id,
'synonym_sgml' => '',
);
$options = array('statement_name' => 'ins_synonym_name_typeid_synonymsgml');
$success = tripal_core_chado_insert('synonym', $values, $options);
if (!$success) {
watchdog("T_gff3_loader", "Cannot add alias $alias to synonym table", array(), WATCHDOG_WARNING);
return 0;
}
$options = array('statement_name' => 'sel_synonym_name_typeid');
$result = tripal_core_chado_select('synonym', array('*'), $select, $options);
$synonym = $result[0];
}
else {
$synonym = $result[0];
}
// check to see if we have a NULL publication in the pub table. If not,
// then add one.
// @coder-ignore: non-drupal schema thus table prefixing does not apply
$select = array('uniquename' => 'null');
$options = array('statement_name' => 'sel_pub_uniquename');
$result = tripal_core_chado_select('pub', array('*'), $select, $options);
if (count($result) == 0) {
// prepare the statement
if (!tripal_core_is_sql_prepared('ins_pub_uniquename_typeid')) {
$psql = "PREPARE ins_pub_uniquename_typeid (text, text) AS
INSERT INTO pub (uniquename,type_id) VALUES ('%s',
(SELECT cvterm_id
FROM cvterm CVT
INNER JOIN dbxref DBX on DBX.dbxref_id = CVT.dbxref_id
INNER JOIN db DB on DB.db_id = DBX.db_id
WHERE CVT.name = $1 and DB.name = $2)";
$status = tripal_core_chado_prepare('ins_pub_uniquename_typeid', $psql, args('text', 'text'));
if (!$status) {
watchdog("T_gff3_loader", "Cannot prepare statement 'ins_pub_uniquename_typeid", array(), WATCHDOG_WARNING);
return 0;
}
}
// insert the null pub
$result = db_fetch_object(chado_query("EXECUTE ins_pub_uniquename_typeid ('%s', '%s')", 'null', 'null'));
if (!$result) {
watchdog("T_gff3_loader", "Cannot add null publication needed for setup of alias", array(), WATCHDOG_WARNING);
return 0;
}
$options = array('statement_name' => 'sel_pub_uniquename');
$result = tripal_core_chado_select('pub', array('*'), $select, $options);
$pub = $result[0];
}
else {
$pub = $result[0];
}
// check to see if the synonym exists in the feature_synonym table
// if not, then add it.
$values = array(
'synonym_id' => $synonym->synonym_id,
'feature_id' => $feature->feature_id,
'pub_id' => $pub->pub_id,
);
$columns = array('feature_synonym_id');
$options = array('statement_name' => 'sel_featuresynonym_syfepu');
$result = tripal_core_chado_select('feature_synonym', $columns, $values, $options);
if (count($result) == 0) {
$values = array(
'synonym_id' => $synonym->synonym_id,
'feature_id' => $feature->feature_id,
'pub_id' => $pub->pub_id,
);
$ins_options = array('statement_name' => 'ins_featuresynonym_syfepu');
$success = tripal_core_chado_insert('feature_synonym', $values, $ins_options);
if (!$success) {
watchdog("T_gff3_loader", "Cannot add alias $alias to feature synonym table", array(), WATCHDOG_WARNING);
return 0;
}
}
}
return 1;
}
| tripal_feature_load_gff3_dbxref | ( | $ | feature, |
| $ | dbxrefs | ||
| ) |
Definition at line 996 of file gff_loader.inc.
{
// iterate through each of the dbxrefs
foreach ($dbxrefs as $dbxref) {
// get the database name from the reference. If it doesn't exist then create one.
$ref = explode(":", $dbxref);
$dbname = $ref[0];
$accession = $ref[1];
// first look for the database name if it doesn't exist then create one.
// first check for the fully qualified URI (e.g. DB:<dbname>. If that
// can't be found then look for the name as is. If it still can't be found
// the create the database
$values = array('name' => "DB:$dbname");
$options = array('statement_name' => 'sel_db_name');
$db = tripal_core_chado_select('db', array('db_id'), $values, $options);
if (count($db) == 0) {
$values = array('name' => "$dbname");
$db = tripal_core_chado_select('db', array('db_id'), $values, $options);
}
if (count($db) == 0) {
$values = array(
'name' => $dbname,
'description' => 'Added automatically by the GFF loader'
);
$options = array('statement_name' => 'ins_db_name');
$success = tripal_core_chado_insert('db', $values, $options);
if ($success) {
$values = array('name' => "$dbname");
$options = array('statement_name' => 'sel_db_name');
$db = tripal_core_chado_select('db', array('db_id'), $values, $options);
}
else {
watchdog("T_gff3_loader", "Cannot find or add the database $dbname", array(), WATCHDOG_WARNING);
return 0;
}
}
$db = $db[0];
// now check to see if the accession exists
$values = array(
'accession' => $accession,
'db_id' => $db->db_id
);
$options = array('statement_name' => 'sel_dbxref_accession_dbid');
$dbxref = tripal_core_chado_select('dbxref', array('dbxref_id'), $values, $options);
// if the accession doesn't exist then we want to add it
if (sizeof($dbxref) == 0) {
$values = array(
'db_id' => $db->db_id,
'accession' => $accession,
'version' => ''
);
$options = array('statement_name' => 'ins_dbxref_dbid_accession_version');
$ret = tripal_core_chado_insert('dbxref', $values, $options);
$values = array(
'accession' => $accession,
'db_id' => $db->db_id
);
$options = array('statement_name' => 'sel_dbxref_accession_dbid');
$dbxref = tripal_core_chado_select('dbxref', array('dbxref_id'), $values, $options);
}
$dbxref = $dbxref[0];
// check to see if this feature dbxref already exists
$values = array(
'dbxref_id' => $dbxref->dbxref_id,
'feature_id' => $feature->feature_id
);
$options = array('statement_name' => 'sel_featuredbxref_dbxrefid_featureid');
$fdbx = tripal_core_chado_select('feature_dbxref', array('feature_dbxref_id'), $values, $options);
// now associate this feature with the database reference if it doesn't
// already exist
if (sizeof($fdbx) == 0) {
$values = array(
'dbxref_id' => $dbxref->dbxref_id,
'feature_id' => $feature->feature_id
);
$options = array('statement_name' => 'ins_featuredbxref_dbxrefid_featureid');
$success = tripal_core_chado_insert('feature_dbxref', $values, $options);
if (!$success) {
watchdog("T_gff3_loader", "Failed to insert Dbxref: $dbname:$accession", array(), WATCHDOG_WARNING);
return 0;
}
}
}
return 1;
}
| tripal_feature_load_gff3_derives_from | ( | $ | feature, |
| $ | subject, | ||
| $ | organism | ||
| ) |
Definition at line 839 of file gff_loader.inc.
{
// get the subject type
$values = array(
'organism_id' => $organism->organism_id,
'uniquename' => $subject,
);
$options = array('statement_name' => 'sel_tripalgfftemp_orun');
$result = tripal_core_chado_select('tripal_gff_temp', array('type_name'), $values, $options);
if (count($result) == 0) {
watchdog("T_gff3_loader", "Cannot find subject type for feature in 'derives_from' relationship: %subject", array('%subject' => $subject), WATCHDOG_WARNING);
return '';
}
$subject_type = $result[0]->type_name;
// get the subject feature
$match = array(
'organism_id' => $organism->organism_id,
'uniquename' => $subject,
'type_id' => array(
'name' => $subject_type,
'cv_id' => array(
'name' => 'sequence'
),
),
);
$options = array('statement_name' => 'sel_feature_orunty');
$sfeature = tripal_core_chado_select('feature', array('feature_id'), $match, $options);
if (count($sfeature)==0) {
watchdog('T_gff3_loader', "Could not add 'Derives_from' relationship ".
"for %uniquename and %subject. Subject feature, '%subject', ".
"cannot be found", array('%uniquename' => $feature->uniquename, '%subject' => $subject), WATCHDOG_ERROR);
return;
}
// now check to see if the relationship already exists
$values = array(
'object_id' => $sfeature[0]->feature_id,
'subject_id' => $feature->feature_id,
'type_id' => array(
'cv_id' => array(
'name' => 'relationship'
),
'name' => 'derives_from',
),
'rank' => 0
);
$options = array('statement_name' => 'sel_featurerelationship_objectid_subjectid_typeid_rank');
$rel = tripal_core_chado_select('feature_relationship', array('*'), $values, $options);
if (count($rel) > 0) {
return;
}
// finally insert the relationship if it doesn't exist
$options = array('statement_name' => 'ins_featurerelationship_objectid_subjectid_typeid_rank');
$ret = tripal_core_chado_insert('feature_relationship', $values, $options);
if (!$ret) {
watchdog("T_gff3_loader", "Could not add 'Derives_from' relationship for $feature->uniquename and $subject",
array(), WATCHDOG_WARNING);
}
}
| tripal_feature_load_gff3_feature | ( | $ | organism, |
| $ | analysis_id, | ||
| $ | cvterm, | ||
| $ | uniquename, | ||
| $ | name, | ||
| $ | residues, | ||
| $ | is_analysis = 'f', |
||
| $ | is_obsolete = 'f', |
||
| $ | add_only, | ||
| $ | score | ||
| ) |
Definition at line 1330 of file gff_loader.inc.
{
// check to see if the feature already exists
$feature = NULL;
$fselect = array(
'organism_id' => $organism->organism_id,
'uniquename' => $uniquename,
'type_id' => $cvterm->cvterm_id
);
$options = array('statement_name' => 'sel_feature_orunty');
$columns = array('feature_id', 'name', 'uniquename', 'seqlen', 'organism_id', 'type_id');
$result = tripal_core_chado_select('feature', $columns, $fselect, $options);
if (count($result) > 0) {
$feature = $result[0];
}
if (strcmp($is_obsolete, 'f')==0 or $is_obsolete == 0) {
$is_obsolete = 'FALSE';
}
if (strcmp($is_obsolete, 't')==0 or $is_obsolete == 1) {
$is_obsolete = 'TRUE';
}
if (strcmp($is_analysis, 'f')==0 or $is_analysis == 0) {
$is_analysis = 'FALSE';
}
if (strcmp($is_analysis, 't')==0 or $is_analysis == 1) {
$is_analysis = 'TRUE';
}
// insert the feature if it does not exist otherwise perform an update
if (!$feature) {
$values = array(
'organism_id' => $organism->organism_id,
'name' => $name,
'uniquename' => $uniquename,
// 'residues' => $residues,
// 'seqlen' => drupal_strlen($residues),
'md5checksum' => md5($residues),
'type_id' => $cvterm->cvterm_id,
'is_analysis' => $is_analysis,
'is_obsolete' => $is_obsolete,
);
$options = array('statement_name' => 'ins_feature_all');
$result = tripal_core_chado_insert('feature', $values, $options);
if (!$result) {
watchdog("T_gff3_loader", "Failed to insert feature '$uniquename' ($cvterm->name)", array(), WATCHDOG_WARNING);
return 0;
}
}
elseif (!$add_only) {
$values = array(
'name' => $name,
// 'residues' => $residues,
// 'seqlen' => drupal_strlen($residues),
'md5checksum' => md5($residues),
'is_analysis' => $is_analysis,
'is_obsolete' => $is_obsolete,
);
$match = array(
'organism_id' => $organism->organism_id,
'uniquename' => $uniquename,
'type_id' => $cvterm->cvterm_id,
);
$options = array('statement_name' => 'upd_feature');
$result = tripal_core_chado_update('feature', $match, $values, $options);
if (!$result) {
watchdog("T_gff3_loader", "Failed to update feature '$uniquename' ($cvterm->name)", array(), WATCHDOG_WARNING);
return 0;
}
}
else {
// the feature exists and we don't want to update it so return
// a value of 0. This will stop all downstream property additions
return 0;
}
// get the newly added feature
$options = array('statement_name' => 'sel_feature_orunty');
$columns = array('feature_id', 'name', 'uniquename', 'seqlen', 'organism_id', 'type_id');
$result = tripal_core_chado_select('feature', $columns, $fselect, $options);
$feature = $result[0];
// add the analysisfeature entry to the analysisfeature table if it doesn't already exist
$af_values = array(
'analysis_id' => $analysis_id,
'feature_id' => $feature->feature_id
);
$options = array('statement_name' => 'sel_analysisfeature_analysisid_featureid');
$afeature = tripal_core_chado_select('analysisfeature', array('analysisfeature_id'), $af_values, $options);
if (count($afeature)==0) {
// if a score is available then set that to be the significance field
if (strcmp($score, '.') != 0) {
$af_values['significance'] = $score;
$options = array('statement_name' => 'ins_analysisfeature_analysisid_featureid_significance');
}
else {
$options = array('statement_name' => 'ins_analysisfeature_analysisid_featureid');
}
if (!tripal_core_chado_insert('analysisfeature', $af_values, $options)) {
watchdog("T_gff3_loader", "Could not add analysisfeature record: $analysis_id, $feature->feature_id", array(), WATCHDOG_WARNING);
}
}
else {
// if a score is available then set that to be the significance field
$new_vals = array();
if (strcmp($score, '.')!=0) {
$new_vals['significance'] = $score;
}
else {
$new_vals['significance'] = '__NULL__';
}
if (!$add_only) {
$options = array('statement_name' => 'upd_analysisfeature');
$ret = tripal_core_chado_update('analysisfeature', $af_values, $new_vals, $options);
if (!$ret) {
watchdog("T_gff3_loader", "Could not update analysisfeature record: $analysis_id, $feature->feature_id", array(), WATCHDOG_WARNING);
}
}
}
return $feature;
}
| tripal_feature_load_gff3_featureloc | ( | $ | feature, |
| $ | organism, | ||
| $ | landmark, | ||
| $ | fmin, | ||
| $ | fmax, | ||
| $ | strand, | ||
| $ | phase, | ||
| $ | is_fmin_partial, | ||
| $ | is_fmax_partial, | ||
| $ | residue_info, | ||
| $ | locgroup, | ||
| $ | landmark_type_id = '', |
||
| $ | landmark_organism_id = '', |
||
| $ | create_landmark = 0, |
||
| $ | landmark_is_target = 0 |
||
| ) |
Definition at line 1458 of file gff_loader.inc.
{
$select = array(
'organism_id' => $landmark_organism_id ? $landmark_organism_id : $organism->organism_id,
'uniquename' => $landmark,
);
$options = array('statement_name' => 'sel_feature_orun');
if ($landmark_type_id) {
$select['type_id'] = $landmark_type_id;
$options = array('statement_name' => 'sel_feature_orunty');
}
$results = tripal_core_chado_select('feature', array('feature_id'), $select, $options);
$srcfeature = '';
if (count($results)==0) {
// so we couldn't find the landmark using the uniquename. Let's try the 'name'.
// if we return only a single result then we can proceed. Otherwise give an
$select = array(
'organism_id' => $landmark_organism_id ? $landmark_organism_id : $organism->organism_id,
'name' => $landmark,
);
$options = array('statement_name' => 'sel_feature_orna');
if ($landmark_type_id) {
$select['type_id'] = $landmark_type_id;
$options = array('statement_name' => 'sel_feature_ornaty');
}
$results = tripal_core_chado_select('feature', array('feature_id'), $select, $options);
if (count($results) == 0) {
// if the landmark is the target feature in a matched alignment then try one more time to
// find it by querying any feature with the same uniquename. If we find one then use it.
if ($landmark_is_target) {
$select = array('uniquename' => $landmark);
$options = array('statement_name' => 'sel_feature_un');
$results = tripal_core_chado_select('feature', array('feature_id'), $select, $options);
if (count($results) == 1) {
$srcfeature = $results[0];
}
}
if (!$srcfeature) {
// we couldn't find the landmark feature, so if the user has requested we create it then do so
// but only if we have a type id
if ($create_landmark and $landmark_type_id) {
$values = array(
'organism_id' => $landmark_organism_id ? $landmark_organism_id : $organism->organism_id,
'name' => $landmark,
'uniquename' => $landmark,
'type_id' => $landmark_type_id
);
$options = array('statement_name' => 'ins_feature_ornaunty');
$results = tripal_core_chado_insert('feature', $values, $options);
if (!$results) {
watchdog("T_gff3_loader", "Cannot find landmark feature: '%landmark', nor could it be inserted",
array('%landmark' => $landmark), WATCHDOG_WARNING);
return 0;
}
$srcfeature = new stdClass();
$srcfeature->feature_id = $results['feature_id'];
}
else {
watchdog("T_gff3_loader", "Cannot find unique landmark feature: '%landmark'.",
array('%landmark' => $landmark), WATCHDOG_WARNING);
return 0;
}
}
}
elseif (count($results) > 1) {
watchdog("T_gff3_loader", "multiple landmarks exist with the name: '%landmark'. Cannot
resolve which one to use. Cannot add the feature location record",
array('%landmark' => $landmark), WATCHDOG_WARNING);
return 0;
}
else {
$srcfeature = $results[0];
}
}
elseif (count($results) > 1) {
watchdog("T_gff3_loader", "multiple landmarks exist with the name: '%landmark'. Cannot
resolve which one to use. Cannot add the feature location record",
array('%landmark' => $landmark), WATCHDOG_WARNING);
return 0;
}
else {
$srcfeature = $results[0];
}
// TODO: create an attribute that recognizes the residue_info,locgroup,
// is_fmin_partial and is_fmax_partial, right now these are
// hardcoded to be false and 0 below.
// check to see if this featureloc already exists, but also keep track of the
// last rank value
$rank = 0;
$exists = 0;
$select = array('feature_id' => $feature->feature_id);
$options = array(
'statement_name' => 'sel_featureloc_fe',
'order_by' => array(
'rank' => 'ASC'
),
);
$locrecs = tripal_core_chado_select('featureloc', array('*'), $select, $options);
foreach ($locrecs as $featureloc) {
// it is possible for the featureloc->srcfeature_id to be NULL. This can happen if the srcfeature
// is not known (according to chado table field descriptions). If it's null then just skip this entry
if (!$featureloc->srcfeature_id) {
continue;
}
$select = array('feature_id' => $featureloc->srcfeature_id);
$options = array('statement_name' => 'sel_feature_fe');
$columns = array('feature_id', 'name');
$locsfeature = tripal_core_chado_select('feature', $columns, $select, $options);
// the source feature name and at least the fmin and fmax must be the same
// for an update of the featureloc, otherwise we'll insert a new record.
if (strcmp($locsfeature[0]->name, $landmark)==0 and
($featureloc->fmin == $fmin or $featureloc->fmax == $fmax)) {
$match = array('featureloc_id' => $featureloc->featureloc_id);
$values = array();
$exists = 1;
if ($featureloc->fmin != $fmin) {
$values['fmin'] = $fmin;
}
if ($featureloc->fmax != $fmax) {
$values['fmax'] = $fmax;
}
if ($featureloc->strand != $strand) {
$values['strand'] = $strand;
}
if (count($values) > 0) {
$options = array('statement_name' => 'upd_featureloc_all');
tripal_core_chado_update('featureloc', $match, $values, $options);
}
}
$rank = $featureloc->rank + 1;
}
if (!$exists) {
// this feature location is new so add it
if (strcmp($is_fmin_partial, 'f')==0 or !$is_fmin_partial) {
$is_fmin_partial = 'FALSE';
}
elseif (strcmp($is_fmin_partial, 't')==0 or $is_fmin_partial = 1) {
$is_fmin_partial = 'TRUE';
}
if (strcmp($is_fmax_partial, 'f')==0 or !$is_fmax_partial) {
$is_fmax_partial = 'FALSE';
}
elseif (strcmp($is_fmax_partial, 't')==0 or $is_fmax_partial = 1) {
$is_fmax_partial = 'TRUE';
}
$values = array(
'feature_id' => $feature->feature_id,
'srcfeature_id' => $srcfeature->feature_id,
'fmin' => $fmin,
'is_fmin_partial' => $is_fmin_partial,
'fmax' => $fmax,
'is_fmax_partial' => $is_fmax_partial,
'strand' => $strand,
'residue_info' => $residue_info,
'locgroup' => $locgroup,
'rank' => $rank
);
$options = array('statement_name' => 'ins_featureloc_all');
if ($phase) {
$values['phase'] = $phase;
$options = array('statement_name' => 'ins_featureloc_allphase');
}
$success = tripal_core_chado_insert('featureloc', $values, $options);
if (!$success) {
watchdog("T_gff3_loader", "Failed to insert featureloc", array(), WATCHDOG_WARNING);
exit;
return 0;
}
}
return 1;
}
| tripal_feature_load_gff3_ontology | ( | $ | feature, |
| $ | dbxrefs | ||
| ) |
Definition at line 1092 of file gff_loader.inc.
{
// iterate through each of the dbxrefs
foreach ($dbxrefs as $dbxref) {
// get the database name from the reference. If it doesn't exist then create one.
$ref = explode(":", $dbxref);
$dbname = $ref[0];
$accession = $ref[1];
// first look for the database name
$options = array('statement_name' => 'sel_db_name');
$db = tripal_core_chado_select('db', array('db_id'), array('name' => "DB:$dbname"), $options);
if (sizeof($db) == 0) {
// now look for the name without the 'DB:' prefix.
$db = tripal_core_chado_select('db', array('db_id'), array('name' => "$dbname"), $options);
if (sizeof($db) == 0) {
watchdog("T_gff3_loader", "Database, $dbname, is not present. Cannot associate term: $dbname:$accession", array(), WATCHDOG_WARNING);
return 0;
}
}
$db = $db[0];
// now check to see if the accession exists
$options = array('statement_name' => 'sel_dbxref_accession_dbid');
$dbxref = tripal_core_chado_select('dbxref', array('dbxref_id'),
array('accession' => $accession, 'db_id' => $db->db_id), $options);
if (sizeof($dbxref) == 0) {
watchdog("T_gff3_loader", "Accession, $accession is missing for reference: $dbname:$accession", array(), WATCHDOG_WARNING);
return 0;
}
$dbxref = $dbxref[0];
// now check to see if the cvterm exists
$options = array('statement_name' => 'sel_cvterm_dbxrefid');
$cvterm = tripal_core_chado_select('cvterm', array('cvterm_id'), array(
'dbxref_id' => $dbxref->dbxref_id), $options);
// if it doesn't exist in the cvterm table, look for an alternate id
if (sizeof($cvterm) == 0) {
$options = array('statement_name' => 'sel_cvtermdbxref_dbxrefid');
$cvterm = tripal_core_chado_select('cvterm_dbxref', array('cvterm_id'), array(
'dbxref_id' => $dbxref->dbxref_id), $options);
if (sizeof($cvterm) == 0) {
watchdog("T_gff3_loader", "CV Term is missing for reference: $dbname:$accession", array(), WATCHDOG_WARNING);
return 0;
}
}
$cvterm = $cvterm[0];
// check to see if this feature cvterm already exists
$options = array('statement_name' => 'sel_featurecvterm_cvtermid_featureid');
$fcvt = tripal_core_chado_select('feature_cvterm', array('feature_cvterm_id'),
array('cvterm_id' => $cvterm->cvterm_id, 'feature_id' => $feature->feature_id),
$options);
// now associate this feature with the cvterm if it doesn't already exist
if (sizeof($fcvt)==0) {
$values = array(
'cvterm_id' => $cvterm->cvterm_id,
'feature_id' => $feature->feature_id,
'pub_id' => array(
'uniquename' => 'null',
),
);
$options = array('statement_name' => 'ins_featurecvterm_cvtermid_featureid_pubid');
$success = tripal_core_chado_insert('feature_cvterm', $values, $options);
if (!$success) {
watchdog("T_gff3_loader", "Failed to insert ontology term: $dbname:$accession", array(), WATCHDOG_WARNING);
return 0;
}
}
}
return 1;
}
| tripal_feature_load_gff3_parents | ( | $ | feature, |
| $ | cvterm, | ||
| $ | parents, | ||
| $ | organism_id, | ||
| $ | fmin | ||
| ) |
Definition at line 905 of file gff_loader.inc.
{
$uname = $feature->uniquename;
$type = $cvterm->name;
$rel_type = 'part_of';
// prepare these SQL statements that will be used repeatedly.
if (!tripal_core_is_sql_prepared('sel_cvterm_cvname_cvtname_synonym')) {
$psql = "PREPARE sel_cvterm_cvname_cvtname_synonym (text, text, text) AS
SELECT CVT.cvterm_id
FROM cvterm CVT
INNER JOIN cv CV on CVT.cv_id = CV.cv_id
LEFT JOIN cvtermsynonym CVTS on CVTS.cvterm_id = CVT.cvterm_id
WHERE cv.name = $1 and (CVT.name = $2 or CVTS.synonym = $3)";
$status = tripal_core_chado_prepare('sel_cvterm_cvname_cvtname_synonym', $psql, array('text', 'text' ,'text'));
if (!$status) {
watchdog("T_gff3_loader", "Cannot prepare statement 'sel_cvterm_cvname_cvtname_synonym' for ontology term",
array(), WATCHDOG_WARNING);
return '';
}
}
// iterate through the parents in the list
foreach ($parents as $parent) {
// get the parent cvterm
$values = array(
'organism_id' => $organism_id,
'uniquename' => $parent,
);
$options = array('statement_name' => 'sel_tripalgfftemp_orun');
$result = tripal_core_chado_select('tripal_gff_temp', array('type_name'), $values, $options);
if (count($result) == 0) {
watchdog("T_gff3_loader", "Cannot find parent: %parent", array('%parent' => $parent), WATCHDOG_WARNING);
return '';
}
$parent_type = $result[0]->type_name;
// try to find the parent
$parentcvterm = db_fetch_object(chado_query("EXECUTE sel_cvterm_cvname_cvtname_synonym ('%s', '%s', '%s')", 'sequence', $parent_type, $parent_type));
$relcvterm = db_fetch_object(chado_query("EXECUTE sel_cvterm_cvname_cvtname_synonym ('%s', '%s', '%s')", 'relationship', $rel_type, $rel_type));
$values = array(
'organism_id' => $organism_id,
'uniquename' => $parent,
'type_id' => $parentcvterm->cvterm_id,
);
$options = array('statement_name' => 'sel_feature_orunty');
$result = tripal_core_chado_select('feature', array('feature_id'), $values, $options);
$parent_feature = $result[0];
// if the parent exists then add the relationship otherwise print error and skip
if ($parent_feature) {
// check to see if the relationship already exists
$values = array(
'object_id' => $parent_feature->feature_id,
'subject_id' => $feature->feature_id,
'type_id' => $relcvterm->cvterm_id,
);
$options = array('statement_name' => 'sel_featurerelationship_objectid_subjectid_typeid');
$rel = tripal_core_chado_select('feature_relationship', array('*'), $values, $options);
if (count($rel) > 0) {
}
else {
// the relationship doesn't already exist, so add it.
$values = array(
'subject_id' => $feature->feature_id,
'object_id' => $parent_feature->feature_id,
'type_id' => $relcvterm->cvterm_id,
);
$options = array('statement_name' => 'ins_featurerelationship_subjectid_objectid_typeid');
$result = tripal_core_chado_insert('feature_relationship', $values, $options);
if (!$result) {
watchdog("T_gff3_loader", "Failed to insert feature relationship '$uname' ($type) $rel_type '$parent' ($parent_type)",
array(), WATCHDOG_WARNING);
}
}
}
else {
watchdog("T_gff3_loader", "Cannot establish relationship '$uname' ($type) $rel_type '$parent' ($parent_type): Cannot find the parent",
array(), WATCHDOG_WARNING);
}
}
}
| tripal_feature_load_gff3_property | ( | $ | feature, |
| $ | property, | ||
| $ | value | ||
| ) |
Definition at line 1645 of file gff_loader.inc.
{
// first make sure the cvterm exists. if not, then add it
$select = array(
'name' => $property,
'cv_id' => array(
'name' => 'feature_property',
),
);
$options = array('statement_name' => 'sel_cvterm_name_cvid');
$result = tripal_core_chado_select('cvterm', array('*'), $select, $options);
// if we don't have a property like this already, then add it otherwise, just return
if (count($result) == 0) {
$term = array(
'id' => "null:$property",
'name' => $property,
'namespace' => 'feature_property',
'is_obsolete' => 0,
);
$cvterm = (object) tripal_cv_add_cvterm($term, 'feature_property', 0, 0);
if (!$cvterm) {
watchdog("T_gff3_loader", "Cannot add cvterm, $property", array(), WATCHDOG_WARNING);
return 0;
}
}
else {
$cvterm = $result[0];
}
// check to see if the property already exists for this feature
// if it does but the value is unique then increment the rank and add it.
// if the value is not unique then don't add it.
$add = 1;
$rank = 0;
$select = array(
'feature_id' => $feature->feature_id,
'type_id' => $cvterm->cvterm_id,
);
$options = array(
'statement_name' => 'sel_featureprop_featureid_typeid',
'order_by' => array(
'rank' => 'ASC',
),
);
$results = tripal_core_chado_select('featureprop', array('*'), $select, $options);
foreach ($results as $prop) {
if (strcmp($prop->value, $value)==0) {
$add = NULL; // don't add it, it already exists
}
$rank = $prop->rank + 1;
}
// add the property if we pass the check above
if ($add) {
$values = array(
'feature_id' => $feature->feature_id,
'type_id' => $cvterm->cvterm_id,
'value' => $value,
'rank' => $rank,
);
$options = array('statement_name' => 'ins_featureprop_all');
$result = tripal_core_chado_insert('featureprop', $values, $options);
if (!$result) {
watchdog("T_gff3_loader", "cannot add featureprop, $property", array(), WATCHDOG_WARNING);
}
}
}
1.7.4