Data structures and functions to handle HGVS mutations.
Data structures and functions to handle HGVS mutations.
(->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.
(->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.
(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.
(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.
(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.
(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.
(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.
(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.
(dna-repeated-seqs coord-start coord-end ref ncopy)
(dna-repeated-seqs coord-start coord-end ref ncopy ncopy-other)
Constructor of DNARepeatedSeqs. Throws an exception if any input is illegal.
Constructor of DNARepeatedSeqs. Throws an exception if any input is illegal.
(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.
(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.
(plain this)
Returns a plain map representing the given mutation.
Returns a plain map representing the given mutation.
(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.
(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.
(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.
(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.
(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.
(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.
(protein-repeated-seqs ref-start coord-start ref-end coord-end ncopy)
(protein-repeated-seqs ref-start
coord-start
ref-end
coord-end
ncopy
ncopy-other)
Constructor of ProteinRepeatedSeqs. Throws an exception if any input is illegal.
Constructor of ProteinRepeatedSeqs. Throws an exception if any input is illegal.
(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.
(restore m)
Restores a plain map to a suitable mutation record.
Restores a plain map to a suitable mutation record.
(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.
(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.
(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.
(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.
(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.
(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.
(rna-repeated-seqs coord-start coord-end ref ncopy)
(rna-repeated-seqs coord-start coord-end ref ncopy ncopy-other)
Constructor of RNARepeatedSeqs. Throws an exception if any input is illegal.
Constructor of RNARepeatedSeqs. Throws an exception if any input is illegal.
(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.
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