/** * Here is some samples of how to use the functions * @param SequenceAlignmentInterface $sequenceAlignmentManager * @return Response * @throws \Exception */ public function clustalseqalignment(SequenceAlignmentInterface $sequenceAlignmentManager) { set_time_limit(0); // we never know ... $sequenceAlignmentManager->setFilename("data/clustal.txt"); $sequenceAlignmentManager->setFormat("CLUSTAL"); $sequenceAlignmentManager->parseFile(); // You wanna sort your array ? :) $sequenceAlignmentManager->sortAlpha("ASC"); $sequenceAlSort = $sequenceAlignmentManager->getSeqSet(); // You wanna fetch something ? $oOffset13 = $sequenceAlignmentManager->getSeqSet()->offsetGet(13); // You wanna know the longest sequence ? $iMaxLength = $sequenceAlignmentManager->getMaxiLength(); // You wanna know the number of gaps ? $iNumberGaps = $sequenceAlignmentManager->getGapCount(); // Have the same length ? $bIsFlush = $sequenceAlignmentManager->getIsFlush(); // Char at res 10 (10th sequence) $sCharAtRes = $sequenceAlignmentManager->charAtRes(10, 10); // Substring between two residues in a sequence $sSubstrBwRes = $sequenceAlignmentManager->substrBwRes(10,10); // Converts a column number to a residue number in a sequence $iColToRes = $sequenceAlignmentManager->colToRes(10, 50); // Converts a residue number to a column number in a sequence $iResToCol = $sequenceAlignmentManager->resToCol(10, 47); // Creates a new alignment set from index 5 to 10 $sequenceAlignmentManager->subalign(5, 10); $oSubALign = $sequenceAlignmentManager; // Creates a new alignment with selected indexes $sequenceAlignmentManager->select(1,2,3); $oSelectAlign = $sequenceAlignmentManager; // Determines the index position of both variant and invariant residues according // to a given "percentage threshold" similar to that in the consensus() method. $aResVar = $sequenceAlignmentManager->resVar(); // Returns the consensus string for an alignment set $aConsensus = $sequenceAlignmentManager->consensus(); // Adding a new sequence object $sequenceAlignmentManager->addSequence($oOffset13); $sequenceAlignmentManagerAdd = $sequenceAlignmentManager; // Dropping a sequence $sequenceAlignmentManager->deleteSequence("sp|P04637|P53_HUMAN"); $sequenceAlignmentManagerDel = $sequenceAlignmentManager; return $this->render('default/clustalseqalignment.html.twig', [ 'sequenceAlSort' => $sequenceAlSort, 'offset13' => $oOffset13, 'maxLength' => $iMaxLength, 'numberGaps' => $iNumberGaps, 'isFlush' => $bIsFlush, 'sCharAtRes' => $sCharAtRes, 'sSubstrBwRes' => $sSubstrBwRes, 'colToRes' => $iColToRes, 'resToCol' => $iResToCol, 'subALign' => $oSubALign, 'selectAlign' => $oSelectAlign, 'resVar' => $aResVar, 'consensus' => $aConsensus, 'sequenceAlignmentManagerAdd' => $sequenceAlignmentManagerAdd, 'sequenceAlignmentManagerDel' => $sequenceAlignmentManagerDel ] ); }
Sort sequences :
13th sequence
Length of the longuest sequence
Number of gaps
Do the sequences have the same length ?
Char at res 10 (10th sequence)
Substring between two residues in a sequence
Converts a column number to a residue number in a sequence
Converts a residue number to a column number in a sequence
Creates a new alignment set from index 5 to 10
Creates a new alignment with selected indexes
Determines the index position of both variant and invariant residues according to a given "percentage threshold" similar to that in the consensus() method.
Returns the consensus string for an alignment set
Adding a new sequence object
Dropping a sequence