API Docs for: 0.1.0
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Kmer Class

Defined in: kmer.js:15
Module: KmerJS

Kmer.js is a module for calculating kmer frequencies and sequence probabilities

Constructor

Kmer

()

Defined in kmer.js:15

Methods

binaryToSequence

(
  • x
)
String

Defined in kmer.js:265

Returns a biological sequence from a binary encoding

Parameters:

  • x Number

    An integer encoding of a biological sequence

Returns:

String:

A biological sequence

Throws:

TypeError:

If x is a float

Example:

>var testKmerIndex = 0; // Analogous to sequenceToBinary() example
>kmer.binaryToSequence(testKmerIndex);
'AAAAAAAAA'

constructor

(
  • k
  • letters
)

Defined in kmer.js:23

The constructor method for instantiation

Parameters:

  • k Number

    A value of k to generate the profile and calculate stats with

  • letters String

    A string of characters for the alphabet of the sequences. Defaults to "ACGT";

Throws:

TypeError:

If the number of letters is not > 1

Example:

Kmer = require('kmer.js')
sampleA = new Kmer(9, "ACGT");

frequency

(
  • seq
)
BigNumber

Defined in kmer.js:314

Calculates a frequency of a sequence in the profile

Parameters:

  • seq String

    A sequence to retrieve the relative count/frequency

Returns:

BigNumber:

The frequency (count/totalCounts) of the sequence from the profile

Throws:

TypeError:

If seq is not a kmer (has a length of k)

Example:

>var testKmer = "AAAAAAAAA";
>var testKmerFrequency = kmer.frequency(testKmer); // Returns a BigNumber.js
>console.log( testKmerFrequency.toNumber() );
0.123457

kmerArray

(
  • s
  • k
)
Array

Defined in kmer.js:133

Returns an array of all k-length substrings. Takes a string and a k in that order.

Parameters:

  • s String

    A string to slice into kmers

  • k Number

    An integer length for all resulting substrings

Returns:

Array:

Returns an array of Strings, all of length k, and all substrings of s.

Throws:

TypeError:

If the length of s < k

Example:

var k = 7 var testString = "AAACCCCCGCACCCGCGGGGGTTTCAGCGTGTCG" var allKmersFromTestString = kmer.kmerArray(testString, 9)

probabilityOfSequence

(
  • seq
)
BigNumber

Defined in kmer.js:368

Calculates the Markov chain probability of a sequence from its transition probabilities

Parameters:

  • seq String

    A biological sequence

Returns:

BigNumber:

Returns the Markov-chain probability of the input sequence

Throws:

TypeError:

If there are letters in seq that aren't in the sequence alphabet

Example:

>var testKmer = "AAACCCCCGCACCCGCGGGGGTTTCAGCGTGTCG";
>var testKmerProb = kmer.probabilityOfSequence(testKmer);
>console.log( testKmerProb.toNumber() );
0.000033333888887777710

profileAsArray

(
  • k
  • letters
)
Uint32Array

Defined in kmer.js:108

Returns a 32-bit int array of zeroes, given an alphabet and choice of k

Parameters:

  • k Number

    An integer value with which to generate substrings

  • letters String

    An optional string of letters, effectively the 'alphabet'. Defaults to 'ACGT'

Returns:

Uint32Array:

Returns a typed array of length : letters.length ^ k

Throws:

TypeError:

If the number of letters is not > 1

sequenceToBinary

(
  • s
)
Number

Defined in kmer.js:238

Returns a binary representation/encoding of a biological sequence

Parameters:

  • s String

    A biological sequence to convert into a binary integer

Returns:

Number:

Returns an integer encoding of a k-mer

Throws:

TypeError:

If there are letters in seq that aren't in the sequence alphabet

Example:

>var testKmer = "AAAAAAAAA" // Length of testKmer matches our initial value of k, 9
>var testKmerIndex = kmer.sequenceToBinary(testKmer);
>console.log( kmer.profile[testIndex] );

streamingUpdate

() Through2

Defined in kmer.js:194

This method streams sequence data to update the kmer profile by side-effect

Returns:

Through2:

A through2 stream wrapper

Throws:

TypeError:

If the input stream's objects don't have a .seq attribute

Example:

>var fasta = require('bionode-fasta'); // Bionode-fastq also
>var fs = require('fs');
>fs.createReadStream("/path/to/example.fasta", {encoding: "UTF-8"})
   .pipe(fasta.obj())
   .pipe(kmer.streamingUpdate())
   .on('finish', function(){
       console.log("Done!");
   });
>console.log(kmer.profile)
>var AWS = require('aws-sdk');
>var s3 = new AWS.S3({apiVersion: '2006-03-01'});
>var fasta = require('bionode-fasta');
>var params = {Bucket: 'bucketname', Key: 'path/to/example.fasta'}
>s3.getObject(params).createReadStream()
   .pipe(fasta.obj())
   .pipe(kmer.streamingUpdate())
   .on('finish', function(){
       console.log("Done!");
   });
>console.log(kmer.profile);

TotalProfileCounts

() BigNumber

Defined in kmer.js:293

Sums the counts for the whole profile. It also updates the associated property .totalProfileCounts as a side-effect

Returns:

BigNumber:

Returns a BigNumber.js sum of all counts from the profile array

Example:

>// After a streaming update, the attribute .totalProfileCounts isn't always updated
>console.log( kmer.totalProfileCounts );
0
>kmer.TotalProfileCounts();
10300
>console.log( kmer.totalProfileCounts );
10300

transitionProbability

(
  • seq1
  • seq2
)
BigNumber

Defined in kmer.js:335

Calculates the transition probability of one sequence to the next in a Markov chain

Parameters:

Returns:

BigNumber:

The transition probability of seq1 to seq2

Throws:

TypeError:

If seq2 is not a kmer (has a length of k)

Example:

>var testKmer1 = "AAAAAAAAA";
>var testKmer2 = "AAAAAAAAT";
>var transProbTK1toTK2 = kmer.transitionProbability(testKmer1, testKmer2);
>console.log( transProbTK1toTK2.toNumber() );
0.111048

update

(
  • seq
)

Defined in kmer.js:168

Updates the profile by pure side-effect. No return value

Parameters:

  • seq String

    A String with letters matching the pre-specified alphabet

Throws:

TypeError:

If there are letters in seq that aren't in the sequence alphabet

Properties

alphabet

String

Defined in kmer.js:54

The 'alphabet' of sequence characters to use

Default: "ACGT"

binaryToLetter

Array

Defined in kmer.js:79

A mapping of binary encoded sequences to their corresponding Strings

k

Number

Defined in kmer.js:47

Choice of k used to instantiate, used throughout the instance methods

letterToBinary

Object

Defined in kmer.js:69

A mapping of letters to their binary encodings (integer indices)

notInAlphabet

RegExp

Defined in kmer.js:62

A regular expression to match characters not belonging to the alphabet

profile

Uint32Array

Defined in kmer.js:86

A profile of kmer counts

totalProfileCounts

BigNumber

Defined in kmer.js:93

A total of counts from an instantiated profile Relies on data being loaded through the streamingUpdate() method Recalculate after updating by running the TotalProfileCounts() method