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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

equivclj/s

(equiv mutation1 mutation2)
source

Equivalenceclj/sprotocol

equiv*clj/s

(equiv* this o)
source

long-amino-acidsclj/s

A list of three-letter amino acids.

A list of three-letter amino acids.
sourceraw docstring

Mutationclj/sprotocol

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

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

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

SeparatelyFormatclj/sprotocol

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

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