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namespace DispatchModule;
/**
* Sequence is an envelope holding information about one specific sequence
*/
class Sequence {
/**
* String of nucleotide sequence
* @var string
*/
public $sequence;
/**
* Statistics from similarity search
* @var array
*/
public $matches = array();
/**
* Biological identifier
* @var string
*/
public $accession;
/**
* Sequence region start
* @var int
*/
public $startPosition;
/**
* Sequence region stop
* @var int
*/
public $stopPosition;
/**
* Length of sequence
* @var int
*/
public $regionLength;
/**
* Source dataset
* @var string
*/
public $dataset;
/**
* SILVA quality indicator (combination of ambig./homopol./vec.contam.)
* @var double
*/
public $sequenceQuality;
/**
* % of ambiguously sequenced nucleotides
* @var double
*/
public $ambiguities;
/**
* % of homopolymers longer than 4 nt.
* @var double
*/
public $homopolymers;
/**
* % of sequence contaminated by vector
* @var double
*/
public $vectorContamination;
/**
* Conservancy indicator
* @var double
*/
public $alignmentQuality;
/**
* SILVA-specific: possible base pairs in common with SILVA ref. structure
* @var int
*/
public $basePairScore;
/**
* Number of seq. bases aligned to within rRNA gene
* @var int
*/
public $alignedBases;
/**
* Confidence that sequence is not anomalous
* @var int
*/
public $pintailQuality;
/**
* Often contains 16S/23S/... info
* @var string
*/
public $description;
/**
* Sequence source molecule type (rRNA, mRNA, DNA, etc.)
* @var string
*/
public $moleculeType;
/**
* ENA data class annotation
* @var string
*/
public $dataClass;
/**
* ENA taxonomic division annotation
* @var string
*/
public $taxonomicDivision;
/**
* Version of the record in ENA database
* @var int
*/
public $version;
/**
* Date when it was first published
* @var timestamp
*/
public $firstPublic;
/**
* Date of the last update
* @var timestamp
*/
public $lastUpdated;
/**
* Identifier of the last release within this record has been updated
* @var string
*/
public $lastUpdatedRelease;
/**
* Author’s comment
* @var string
*/
public $comment;
/**
* Name of current specie
* @var string
*/
public $name;
/**
*
* @var string
*/
public $pathName;
/**
* Contains names of all of node’s ancestors recursively from the root.
* By default separated by a semicolon.
* @var string
*/
public $annotationSource;
/**
* Allows to classify items
* @var int
*/
public $state;
/**
* Contains information about references (ie. an article, paper,...)
* @var array
*/
public $references;
/**
* Unions some properties of a region of a nucleotide sequence (part of a gene)
* @var array
*/
public $features;
/**
* Contains data about references (links) to external databases.
* Reference can be stored for annotaion (reference to a DB) or annotation reference (journal, webpage) as well
* @var array
*/
public $xrefs;
/**
* Contains information about secondary structure prediction
* @var array
*/
public $predictions;
/**
* Loads data from array into properties
*
* @param array $data array containing values indexed by attributes (properties) name
*/
public function loadData(array $data, $object = null) {
if ($object == null) { $object = $this; }
foreach ($data as $name => $value) {
if (property_exists($object, $name)) {
if (is_array($value)) {
foreach ($value as $k => $arr) {
if (is_array($arr)) {
foreach ($arr as $key => $innerVal) {
$value[$k][$key] = $this->addOrdinal($innerVal);
}
} else {
$value[$k] = $this->addOrdinal($arr);
}
}
$object->$name = $value;
} else {
$object->$name = $this->addOrdinal($value);
}
} else if ($name == 'match') {
$match = new \DispatchModule\BaseMatch($value['label']);
$this->loadData($value, $match);
$this->matches[] = $match;
}
}
}
/**
* Adds preformated value - date/array/formated string
*
* @param mixed $data
* @return mixed
*/
protected function addOrdinal($data) {
if (is_a($data, 'Nette\DateTime')) {
$date = new \DateTime($data);
$return = $date->format('d. m. Y');
} elseif (is_array($data)) {
$return = $data;
} else {
$return = $this->formatString($data);
}
return $return;
}
/**
* Formats string for displaying (newlines, etc)
*
* @param string $string
* @return string
*/
protected function formatString($string) {
if ((string) $string == '') {
$result = null;
} else {
$semicolonSpaces = str_replace(';', '; ', (string) $string);
$order = array("\r\n", "\n", "/n", "\r");
$result = str_replace($order, '<br />', $semicolonSpaces);
}
return $result;
}
/**
* Converts nested array into one string line. If it is a string than the same string is returned. If not string like key:value1|value2|key2:value1||value2 is returned
* @param string|array $object Object to process
* @param int $depth Depth of the array
* @return string
*/
private function getOneDimension($object, $depth = 1) {
if ($object instanceof \DispatchModule\BaseMatch) {
$object = get_object_vars($object);
}
if (!is_array($object)) {
return $object;
}
$returnLine = "";
foreach ($object as $key => $value) {
if (!empty($returnLine)) {
$returnLine .= str_repeat("|", $depth);
}
if (!is_numeric($key)) {
$returnLine .= $key . ":";
}
$returnLine .= $this->getOneDimension($value, $depth + 1);
}
return $returnLine;
}
/**
* Converts Sequence object into one dimensional array
* @return array One dimensional array
*/
public function convertIntoOneDimensionalArray() {
$result = array();
foreach (get_object_vars($this) as $key => $value) {
$result[$key] = $this->getOneDimension($value);
}
return $result;
}
/**
* Gets all info about sequence from database
*
* @param \DispatchModule\SearchParser $searchParser instance of search parser
* @param string $accession accession number
* @param int $start (optional) start position
* @param int $stop (optional) stop position
* @return array sequence data
* @throws \BaseModule\Exceptions\NotFoundException
*/
public static function loadSequenceInfo($searchParser, $accession, $start = null, $stop = null) {
$f = new \BaseModule\Form();
$f->addHidden('db_accession', $accession);
if ($start !== null) {
$f->addHidden('db_start', $start);
}
if ($stop !== null) {
$f->addHidden('db_stop', $stop);
}
$f->addHidden('db', true);
$resultSet = $searchParser->parseForm($f);
$data = $resultSet->getData();
// load information needed - sequence, secondary structure and idString (accesion_predictionId)
if (empty($data[0]->sequence) || !isset($data[0]->predictions) || empty($data[0]->accession)) {
throw new \BaseModule\Exceptions\NotFoundException('Sequence [accesion=' . $accession . ', ' . $start . '-' . $stop . '] not found');
}
return $data[0];
}
/**
* Gets prediction structure from all sequence predictions
*
* @param array $predictions array containing info about all structure predictions
* @param int $prediction_id id of prediction to get
* @return string prediction structure
* @throws \BaseModule\Exceptions\NotFoundException
*/
public static function getPredictionFromGroup($predictions, $prediction_id) {
foreach ($predictions as $prediction) {
if ($prediction['structure_id'] == $prediction_id) {
$resultPrediction = $prediction['structure'];
}
}
if (empty($resultPrediction)) {
throw new \BaseModule\Exceptions\NotFoundException('Prediction not found');
}
return $resultPrediction;
}
/**
* Simplifies the prediction - converts pseudoknots to ordinary knots ({}, [] -> ())
*
* @param string $complexPrediction prediction including curly braces/brackets
* @return string simple dot-paren string suitable for use in ViennaRNA package
*/
public static function makeSimplePrediction($complexPrediction) {
return str_replace('}', '.', str_replace('{', '.', str_replace(']', '.', str_replace('[', '.', $complexPrediction))));
}
}