clj-hgvs.mutation — clj-hgvs 0.5.0

Data structures and functions to handle HGVS mutations.

->long-amino-acid clj/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.

->short-amino-acid clj/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.

dna-alleles clj/s

(dna-alleles mutations1 mutations2)

dna-conversion clj/s

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

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

dna-deletion clj/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.

dna-duplication clj/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.

dna-indel clj/s

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

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

dna-insertion clj/s

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

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

dna-inversion clj/s

(dna-inversion coord-start coord-end)

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

dna-repeated-seqs clj/s

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

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

dna-substitution clj/s

(dna-substitution coord ref typ)

(dna-substitution coord ref typ alt)

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

equiv clj/s

(equiv mutation1 mutation2)

Equivalence clj/s protocol

equiv* clj/s

(equiv* this o)

long-amino-acids clj/s

A list of three-letter amino acids.

Mutation clj/s protocol

format clj/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.

plain clj/s

(plain this)

Returns a plain map representing the given mutation.

no-protein clj/s

(no-protein)

no-rna clj/s

(no-rna)

parse clj/s

(parse s kind)

parse-dna clj/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.

parse-dna-alleles clj/s

(parse-dna-alleles s kind)

parse-dna-conversion clj/s

(parse-dna-conversion s kind)

parse-dna-deletion clj/s

(parse-dna-deletion s kind)

parse-dna-duplication clj/s

(parse-dna-duplication s kind)

parse-dna-indel clj/s

(parse-dna-indel s kind)

parse-dna-insertion clj/s

(parse-dna-insertion s kind)

parse-dna-inversion clj/s

(parse-dna-inversion s kind)

parse-dna-repeated-seqs clj/s

(parse-dna-repeated-seqs s kind)

parse-dna-substitution clj/s

(parse-dna-substitution s kind)

parse-protein clj/s

(parse-protein s)

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

parse-protein-alleles clj/s

(parse-protein-alleles s)

parse-protein-deletion clj/s

(parse-protein-deletion s)

parse-protein-duplication clj/s

(parse-protein-duplication s)

parse-protein-extension clj/s

(parse-protein-extension s)

parse-protein-frame-shift clj/s

(parse-protein-frame-shift s)

parse-protein-indel clj/s

(parse-protein-indel s)

parse-protein-insertion clj/s

(parse-protein-insertion s)

parse-protein-repeated-seqs clj/s

(parse-protein-repeated-seqs s)

parse-protein-substitution clj/s

(parse-protein-substitution s)

parse-rna clj/s

(parse-rna s)

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

parse-rna-alleles clj/s

(parse-rna-alleles s)

parse-rna-conversion clj/s

(parse-rna-conversion s)

parse-rna-deletion clj/s

(parse-rna-deletion s)

parse-rna-duplication clj/s

(parse-rna-duplication s)

parse-rna-indel clj/s

(parse-rna-indel s)

parse-rna-insertion clj/s

(parse-rna-insertion s)

parse-rna-inversion clj/s

(parse-rna-inversion s)

parse-rna-repeated-seqs clj/s

(parse-rna-repeated-seqs s)

parse-rna-substitution clj/s

(parse-rna-substitution s)

parse-uncertain-mutation clj/s

(parse-uncertain-mutation s kind)

protein-alleles clj/s

(protein-alleles mutations1 mutations2)

protein-deletion clj/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.

protein-duplication clj/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.

protein-extension clj/s

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

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

protein-frame-shift clj/s

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

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

protein-indel clj/s

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

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

protein-insertion clj/s

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

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

protein-no-effect clj/s

(protein-no-effect)

protein-repeated-seqs clj/s

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

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

protein-substitution clj/s

(protein-substitution ref coord alt)

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

protein-unknown-mutation clj/s

(protein-unknown-mutation)

restore clj/s multimethod

(restore m)

Restores a plain map to a suitable mutation record.

rna-alleles clj/s

(rna-alleles mutations1 mutations2)

rna-conversion clj/s

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

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

rna-deletion clj/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.

rna-duplication clj/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.

rna-indel clj/s

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

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

rna-insertion clj/s

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

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

rna-inversion clj/s

(rna-inversion coord-start coord-end)

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

rna-no-effect clj/s

(rna-no-effect)

rna-repeated-seqs clj/s

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

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

rna-splice-affected clj/s

(rna-splice-affected)

rna-substitution clj/s

(rna-substitution coord ref alt)

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

rna-unknown-mutation clj/s

(rna-unknown-mutation)

SeparatelyFormat clj/s protocol

format-common clj/s

(format-common this opts)

format-unique clj/s

(format-unique this opts)

short-amino-acids clj/s

A list of single-letter amino acids.

uncertain-mutation clj/s

(uncertain-mutation mutation)

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