com.milaboratory.core.mutations

Class MutationsUtil

java.lang.Object

com.milaboratory.core.mutations.MutationsUtil

public final class MutationsUtil
extends Object

Author:

Dmitry Bolotin, Stanislav Poslavsky

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MutationsUtil.MutationNt2AADescriptor
static class	MutationsUtil.MutationsWitMapping

Method Summary

Methods

Modifier and Type	Method and Description
static int[]	btopDecode(String alignment, Alphabet alphabet) Decodes btop-encoded mutations.
static boolean	check(int[] mutations)
static boolean	check(Mutations mutations)
static int[]	decode(String mutations, Alphabet alphabet) Decodes mutations encoded using format described in Mutation.encode(int, com.milaboratory.core.sequence.Alphabet).
static String	encode(int[] mutations, Alphabet alphabet) Encodes mutations in compact human-readable string, that can be decoded by method decode(String, com.milaboratory.core.sequence.Alphabet).
static String	encode(int[] mutations, Alphabet alphabet, String separator) Encodes mutations in compact human-readable string, that can be decoded by method decode(String, com.milaboratory.core.sequence.Alphabet).
static String	encodeFixed(int[] mutations, Alphabet alphabet)
static <S extends Sequence> boolean	isCompatibleWithSequence(S sequence, int[] mutations)
static boolean	isSorted(int[] mutations)
static NSequenceWithQuality	mutate(NSequenceWithQuality seq, Mutations<NucleotideSequence> mutations)
static Mutations<AminoAcidSequence>	nt2aa(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters)
static Mutations<AminoAcidSequence>	nt2aa(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets)
static MutationsUtil.MutationNt2AADescriptor[]	nt2aaDetailed(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets) Performs a comprehensive translation of mutations present in a nucleotide sequence to effective mutations in corresponding amino acid sequence.
static MutationsUtil.MutationsWitMapping	nt2aaWithMapping(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets)
static int[]	nt2IndividualAA(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters)
static void	shiftIndelsAtHomopolymers(Sequence seq1, int[] mutations) This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels randomly along such regions Required for filterMutations algorithm to work correctly Works inplace
static void	shiftIndelsAtHomopolymers(Sequence seq1, int seq1From, int[] mutations) This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels randomly along such regions Required for filterMutations algorithm to work correctly Works inplace
static <S extends Sequence<S>> Mutations<S>	shiftIndelsAtHomopolymers(S seq1, int seq1From, Mutations<S> mutations) This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels randomly along such regions Required for filterMutations algorithm to work correctly Works inplace
static <S extends Sequence<S>> Mutations<S>	shiftIndelsAtHomopolymers(S seq1, Mutations<S> mutations) This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels randomly along such regions Required for filterMutations algorithm to work correctly Works inplace

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

mutate

public static NSequenceWithQuality mutate(NSequenceWithQuality seq,
                          Mutations<NucleotideSequence> mutations)

shiftIndelsAtHomopolymers

public static <S extends Sequence<S>> Mutations<S> shiftIndelsAtHomopolymers(S seq1,
                                                             Mutations<S> mutations)

This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels randomly along such regions Required for filterMutations algorithm to work correctly Works inplace

Parameters:

seq1 - reference sequence for the mutations

mutations - array of mutations

shiftIndelsAtHomopolymers

public static <S extends Sequence<S>> Mutations<S> shiftIndelsAtHomopolymers(S seq1,
                                                             int seq1From,
                                                             Mutations<S> mutations)

This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels randomly along such regions Required for filterMutations algorithm to work correctly Works inplace

Parameters:

seq1 - reference sequence for the mutations

seq1From - seq1 from

mutations - array of mutations

shiftIndelsAtHomopolymers

public static void shiftIndelsAtHomopolymers(Sequence seq1,
                             int[] mutations)

This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels randomly along such regions Required for filterMutations algorithm to work correctly Works inplace

Parameters:

seq1 - reference sequence for the mutations

mutations - array of mutations

shiftIndelsAtHomopolymers

public static void shiftIndelsAtHomopolymers(Sequence seq1,
                             int seq1From,
                             int[] mutations)

This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels randomly along such regions Required for filterMutations algorithm to work correctly Works inplace

Parameters:

seq1 - reference sequence for the mutations

seq1From - seq1 from

mutations - array of mutations

check

public static boolean check(Mutations mutations)

check

public static boolean check(int[] mutations)

isSorted

public static boolean isSorted(int[] mutations)

isCompatibleWithSequence

public static <S extends Sequence> boolean isCompatibleWithSequence(S sequence,
                                                    int[] mutations)

encode

public static String encode(int[] mutations,
            Alphabet alphabet)

Encodes mutations in compact human-readable string, that can be decoded by method decode(String, com.milaboratory.core.sequence.Alphabet).

For format see Mutation.encode(int, com.milaboratory.core.sequence.Alphabet).

Mutations are just concatenated. The following RegExp can be used for simple parsing of resulting string for nucleotide sequences: ([SDI])([ATGC]?)(\d+)([ATGC]?) .

Parameters:

mutations - mutations to encode

Returns:

mutations in a human-readable string

encode

public static String encode(int[] mutations,
            Alphabet alphabet,
            String separator)

Encodes mutations in compact human-readable string, that can be decoded by method decode(String, com.milaboratory.core.sequence.Alphabet).

For format see Mutation.encode(int, com.milaboratory.core.sequence.Alphabet).

Mutations are just concatenated with given separator. The following RegExp can be used for simple parsing of resulting string for nucleotide sequences: ([SDI])([ATGC]?)(\d+)([ATGC]?) .

Parameters:

mutations - mutations to encode

separator - separator

Returns:

mutations in a human-readable string

encodeFixed

public static String encodeFixed(int[] mutations,
                 Alphabet alphabet)

decode

public static int[] decode(String mutations,
           Alphabet alphabet)

Decodes mutations encoded using format described in Mutation.encode(int, com.milaboratory.core.sequence.Alphabet).

btopDecode

public static int[] btopDecode(String alignment,
               Alphabet alphabet)

Decodes btop-encoded mutations.

Parameters:

alignment - btop-encoded mutations

Returns:

MiLib mutations

nt2aa

public static Mutations<AminoAcidSequence> nt2aa(NucleotideSequence seq1,
                                 Mutations<NucleotideSequence> mutations,
                                 TranslationParameters translationParameters)

nt2aa

public static Mutations<AminoAcidSequence> nt2aa(NucleotideSequence seq1,
                                 Mutations<NucleotideSequence> mutations,
                                 TranslationParameters translationParameters,
                                 int maxShiftedTriplets)

nt2IndividualAA

public static int[] nt2IndividualAA(NucleotideSequence seq1,
                    Mutations<NucleotideSequence> mutations,
                    TranslationParameters translationParameters)

nt2aaWithMapping

public static MutationsUtil.MutationsWitMapping nt2aaWithMapping(NucleotideSequence seq1,
                                                 Mutations<NucleotideSequence> mutations,
                                                 TranslationParameters translationParameters,
                                                 int maxShiftedTriplets)

nt2aaDetailed

public static MutationsUtil.MutationNt2AADescriptor[] nt2aaDetailed(NucleotideSequence seq1,
                                                    Mutations<NucleotideSequence> mutations,
                                                    TranslationParameters translationParameters,
                                                    int maxShiftedTriplets)

Performs a comprehensive translation of mutations present in a nucleotide sequence to effective mutations in corresponding amino acid sequence.

The resulting array contains:

• the original nucleotide mutation
• "individual" amino acid mutation, i.e. an expected amino acid mutation given no other mutations have occurred
• "cumulative" amino acid mutation, i.e. the observed amino acid mutation combining effect from all other nucleotide mutations

Parameters:

seq1 - the reference nucleotide sequence

mutations - nucleotide mutations in the reference nucleotide sequence

translationParameters - translation parameters

maxShiftedTriplets - max number of shifted triplets for computing the cumulative effect from indels

Returns:

an array of nucleotide mutations with their amino acid translations