\Amelaye\BioPHP\Domain\Tools\ServiceGeneticsFunctions

Class NucleotidsManager

Summary

Methods
Properties
Constants
CountACGT()
countYRWSKMDVHB()
CountCG()
createInversion()
removeNonCodingProt()
No public properties found
No constants found
No protected methods found
No protected properties found
N/A
No private methods found
No private properties found
N/A

Methods

CountACGT()

CountACGT(string  $sSequence) : int

Will count number of A, C, G and T bases in the sequence

Parameters

string $sSequence

is the sequence

Throws

\Exception

Returns

int

countYRWSKMDVHB()

countYRWSKMDVHB(string  $c) : int

Will count number of degenerate nucleotides (Y, R, W, S, K, MD, V, H and B) in the sequence

Parameters

string $c

Throws

\Exception

Returns

int

CountCG()

CountCG( $c) : int

Parameters

$c

Throws

\Exception

Returns

int

createInversion()

createInversion( $sSequence,  $dnaComplements) : mixed

Place sequence and reverse complement of sequence in one line

Parameters

$sSequence
$dnaComplements

Returns

mixed

removeNonCodingProt()

removeNonCodingProt(string  $sSequence) : string

Removes non-coding characters

Parameters

string $sSequence

Throws

\Exception

Returns

string