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clj-hgvs.mutation

Data structures and functions to handle HGVS mutations.

Data structures and functions to handle HGVS mutations.
raw docstring

->long-amino-acidclj/s

(->long-amino-acid s)

Converts a single-letter amino acid into a three-letter one. s must be String or Character. Returns nil if s is not present in amino acid list.

Converts a single-letter amino acid into a three-letter one. s must be String
or Character. Returns nil if s is not present in amino acid list.
sourceraw docstring

->short-amino-acidclj/s

(->short-amino-acid s)

Converts a three-letter amino acid into a single-letter one. s must be String or Character. Returns nil if s is not present in amino acid list.

Converts a three-letter amino acid into a single-letter one. s must be String
or Character. Returns nil if s is not present in amino acid list.
sourceraw docstring

dna-allelesclj/s

(dna-alleles mutations1 mutations2)
source

dna-conversionclj/s

(dna-conversion coord-start coord-end alt)

Constructor of DNAConversion. Throws an exception if any input is illegal.

Constructor of DNAConversion. Throws an exception if any input is illegal.
sourceraw docstring

dna-deletionclj/s

(dna-deletion coord-start coord-end)
(dna-deletion coord-start coord-end ref)

Constructor of DNADeletion. Throws an exception if any input is illegal.

Constructor of DNADeletion. Throws an exception if any input is illegal.
sourceraw docstring

dna-duplicationclj/s

(dna-duplication coord-start coord-end)
(dna-duplication coord-start coord-end ref)

Constructor of DNADuplication. Throws an exception if any input is illegal.

Constructor of DNADuplication. Throws an exception if any input is illegal.
sourceraw docstring

dna-indelclj/s

(dna-indel coord-start coord-end ref alt)

Constructor of DNAIndel. Throws an exception if any input is illegal.

Constructor of DNAIndel. Throws an exception if any input is illegal.
sourceraw docstring

dna-insertionclj/s

(dna-insertion coord-start coord-end alt)

Constructor of DNAInsertion. Throws an exception if any input is illegal.

Constructor of DNAInsertion. Throws an exception if any input is illegal.
sourceraw docstring

dna-inversionclj/s

(dna-inversion coord-start coord-end)

Constructor of DNAInversion. Throws an exception if any input is illegal.

Constructor of DNAInversion. Throws an exception if any input is illegal.
sourceraw docstring

dna-repeated-seqsclj/s

(dna-repeated-seqs coord-start coord-end ref ncopy)

Constructor of DNARepeatedSeqs. Throws an exception if any input is illegal.

Constructor of DNARepeatedSeqs. Throws an exception if any input is illegal.
sourceraw docstring

dna-substitutionclj/s

(dna-substitution coord ref typ)
(dna-substitution coord ref typ alt)

Constructor of DNASubstitution. Throws an exception if any input is illegal.

Constructor of DNASubstitution. Throws an exception if any input is illegal.
sourceraw docstring

DNAAllelescljs

source

DNAConversioncljs

source

DNADeletioncljs

source

DNADuplicationcljs

source

DNAIndelcljs

source

DNAInsertioncljs

source

DNAInversioncljs

source

DNARepeatedSeqscljs

source

DNASubstitutioncljs

source

long-amino-acidsclj/s

A list of three-letter amino acids.

A list of three-letter amino acids.
sourceraw docstring

Mutationclj/s≠protocol

formatclj/s

(format this)
(format this opts)

Returns a string representing the given mutation. The second argument is an optional map to specify style. See document of clj-hgvs.core/format for details of the option.

Returns a string representing the given mutation. The second argument is an
optional map to specify style. See document of clj-hgvs.core/format for
details of the option.

plainclj/s

(plain this)

Returns a plain map representing the given mutation.

Returns a plain map representing the given mutation.
source

no-proteinclj/s

(no-protein)
source

no-rnaclj/s

(no-rna)
source

NoProteincljs

source

NoRNAcljs

source

parseclj/s

(parse s kind)
source

parse-dnaclj/s

(parse-dna s kind)

Parses a DNA mutation string s, returning a record implementing Mutation protocol. kind must be selected from :genome, :mitochondria, :coding-dna, or :non-coding-dna.

Parses a DNA mutation string s, returning a record implementing Mutation
protocol. kind must be selected from :genome, :mitochondria, :coding-dna, or
:non-coding-dna.
sourceraw docstring

parse-dna-allelesclj/s

(parse-dna-alleles s kind)
source

parse-dna-conversionclj/s

(parse-dna-conversion s kind)
source

parse-dna-deletionclj/s

(parse-dna-deletion s kind)
source

parse-dna-duplicationclj/s

(parse-dna-duplication s kind)
source

parse-dna-indelclj/s

(parse-dna-indel s kind)
source

parse-dna-insertionclj/s

(parse-dna-insertion s kind)
source

parse-dna-inversionclj/s

(parse-dna-inversion s kind)
source

parse-dna-repeated-seqsclj/s

(parse-dna-repeated-seqs s kind)
source

parse-dna-substitutionclj/s

(parse-dna-substitution s kind)
source

parse-proteinclj/s

(parse-protein s)

Parses a protein mutation string s, returning a record implementing Mutation protocol.

Parses a protein mutation string s, returning a record implementing Mutation
protocol.
sourceraw docstring

parse-protein-allelesclj/s

(parse-protein-alleles s)
source

parse-protein-deletionclj/s

(parse-protein-deletion s)
source

parse-protein-duplicationclj/s

(parse-protein-duplication s)
source

parse-protein-extensionclj/s

(parse-protein-extension s)
source

parse-protein-frame-shiftclj/s

(parse-protein-frame-shift s)
source

parse-protein-indelclj/s

(parse-protein-indel s)
source

parse-protein-insertionclj/s

(parse-protein-insertion s)
source

parse-protein-repeated-seqsclj/s

(parse-protein-repeated-seqs s)
source

parse-protein-substitutionclj/s

(parse-protein-substitution s)
source

parse-rnaclj/s

(parse-rna s)

Parses a RNA mutation string s, returning a record implementing Mutation protocol.

Parses a RNA mutation string s, returning a record implementing Mutation
protocol.
sourceraw docstring

parse-rna-allelesclj/s

(parse-rna-alleles s)
source

parse-rna-conversionclj/s

(parse-rna-conversion s)
source

parse-rna-deletionclj/s

(parse-rna-deletion s)
source

parse-rna-duplicationclj/s

(parse-rna-duplication s)
source

parse-rna-indelclj/s

(parse-rna-indel s)
source

parse-rna-insertionclj/s

(parse-rna-insertion s)
source

parse-rna-inversionclj/s

(parse-rna-inversion s)
source

parse-rna-repeated-seqsclj/s

(parse-rna-repeated-seqs s)
source

parse-rna-substitutionclj/s

(parse-rna-substitution s)
source

parse-uncertain-mutationclj/s

(parse-uncertain-mutation s kind)
source

protein-allelesclj/s

(protein-alleles mutations1 mutations2)
source

protein-deletionclj/s

(protein-deletion ref-start coord-start)
(protein-deletion ref-start coord-start ref-end coord-end)

Constructor of ProteinDeletion. Throws an exception if any input is illegal.

Constructor of ProteinDeletion. Throws an exception if any input is illegal.
sourceraw docstring

protein-duplicationclj/s

(protein-duplication ref-start coord-start)
(protein-duplication ref-start coord-start ref-end coord-end)

Constructor of ProteinDuplication. Throws an exception if any input is illegal.

Constructor of ProteinDuplication. Throws an exception if any input is illegal.
sourceraw docstring

protein-extensionclj/s

(protein-extension ref coord alt region new-site)

Constructor of ProteinExtension. Throws an exception if any input is illegal.

Constructor of ProteinExtension. Throws an exception if any input is illegal.
sourceraw docstring

protein-frame-shiftclj/s

(protein-frame-shift ref coord alt new-ter-site)

Constructor of ProteinFrameShift. Throws an exception if any input is illegal.

Constructor of ProteinFrameShift. Throws an exception if any input is illegal.
sourceraw docstring

protein-indelclj/s

(protein-indel ref-start coord-start ref-end coord-end alts)

Constructor of ProteinIndel. Throws an exception if any input is illegal.

Constructor of ProteinIndel. Throws an exception if any input is illegal.
sourceraw docstring

protein-insertionclj/s

(protein-insertion ref-start coord-start ref-end coord-end alts)

Constructor of ProteinInsertion. Throws an exception if any input is illegal.

Constructor of ProteinInsertion. Throws an exception if any input is illegal.
sourceraw docstring

protein-no-effectclj/s

(protein-no-effect)
source

protein-repeated-seqsclj/s

(protein-repeated-seqs ref-start coord-start ref-end coord-end ncopy)

Constructor of ProteinRepeatedSeqs. Throws an exception if any input is illegal.

Constructor of ProteinRepeatedSeqs. Throws an exception if any input is illegal.
sourceraw docstring

protein-substitutionclj/s

(protein-substitution ref coord alt)

Constructor of ProteinSubstitution. Throws an exception if any input is illegal.

Constructor of ProteinSubstitution. Throws an exception if any input is illegal.
sourceraw docstring

protein-unknown-mutationclj/s

(protein-unknown-mutation)
source

ProteinAllelescljs

source

ProteinDeletioncljs

source

ProteinDuplicationcljs

source

ProteinExtensioncljs

source

ProteinFrameShiftcljs

source

ProteinIndelcljs

source

ProteinInsertioncljs

source

ProteinNoEffectcljs

source

ProteinRepeatedSeqscljs

source

ProteinSubstitutioncljs

source

ProteinUnknownMutationcljs

source

restoreclj/smultimethod

(restore m)

Restores a plain map to a suitable mutation record.

Restores a plain map to a suitable mutation record.
sourceraw docstring

rna-allelesclj/s

(rna-alleles mutations1 mutations2)
source

rna-conversionclj/s

(rna-conversion coord-start coord-end alt)

Constructor of RNAConversion. Throws an exception if any input is illegal.

Constructor of RNAConversion. Throws an exception if any input is illegal.
sourceraw docstring

rna-deletionclj/s

(rna-deletion coord-start coord-end)
(rna-deletion coord-start coord-end ref)

Constructor of DNAdeletion. Throws an exception if any input is illegal.

Constructor of DNAdeletion. Throws an exception if any input is illegal.
sourceraw docstring

rna-duplicationclj/s

(rna-duplication coord-start coord-end)
(rna-duplication coord-start coord-end ref)

Constructor of RNADuplication. Throws an exception if any input is illegal.

Constructor of RNADuplication. Throws an exception if any input is illegal.
sourceraw docstring

rna-indelclj/s

(rna-indel coord-start coord-end ref alt)

Constructor of RNAIndel. Throws an exception if any input is illegal.

Constructor of RNAIndel. Throws an exception if any input is illegal.
sourceraw docstring

rna-insertionclj/s

(rna-insertion coord-start coord-end alt)

Constructor of RNAInsertion. Throws an exception if any input is illegal.

Constructor of RNAInsertion. Throws an exception if any input is illegal.
sourceraw docstring

rna-inversionclj/s

(rna-inversion coord-start coord-end)

Constructor of RNAInversion. Throws an exception if any input is illegal.

Constructor of RNAInversion. Throws an exception if any input is illegal.
sourceraw docstring

rna-no-effectclj/s

(rna-no-effect)
source

rna-repeated-seqsclj/s

(rna-repeated-seqs coord-start coord-end ref ncopy)

Constructor of RNARepeatedSeqs. Throws an exception if any input is illegal.

Constructor of RNARepeatedSeqs. Throws an exception if any input is illegal.
sourceraw docstring

rna-splice-affectedclj/s

(rna-splice-affected)
source

rna-substitutionclj/s

(rna-substitution coord ref alt)

Constructor of RNASubstitution. Throws an exception if any input is illegal.

Constructor of RNASubstitution. Throws an exception if any input is illegal.
sourceraw docstring

rna-unknown-mutationclj/s

(rna-unknown-mutation)
source

RNAAllelescljs

source

RNAConversioncljs

source

RNADeletioncljs

source

RNADuplicationcljs

source

RNAIndelcljs

source

RNAInsertioncljs

source

RNAInversioncljs

source

RNANoEffectcljs

source

RNARepeatedSeqscljs

source

RNASpliceAffectedcljs

source

RNASubstitutioncljs

source

RNAUnknownMutationcljs

source

SeparatelyFormatclj/s≠protocol

format-commonclj/s

(format-common this opts)

format-uniqueclj/s

(format-unique this opts)
source

short-amino-acidsclj/s

A list of single-letter amino acids.

A list of single-letter amino acids.
sourceraw docstring

uncertain-mutationclj/s

(uncertain-mutation mutation)

Constructor of UncertainMutation. Throws an exception if any input is illegal.

Constructor of UncertainMutation. Throws an exception if any input is
illegal.
sourceraw docstring

UncertainMutationcljs

source

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