clj-hgvs.mutation
Data structures and functions to handle HGVS mutations.
->long-amino-acid
(->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
(->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
(dna-alleles mutations1 mutations2)
dna-conversion
(dna-conversion coord-start coord-end alt)
Constructor of DNAConversion. Throws an exception if any input is illegal.
dna-deletion
(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
(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
(dna-indel coord-start coord-end ref alt)
Constructor of DNAIndel. Throws an exception if any input is illegal.
dna-insertion
(dna-insertion coord-start coord-end alt)
Constructor of DNAInsertion. Throws an exception if any input is illegal.
dna-inversion
(dna-inversion coord-start coord-end)
Constructor of DNAInversion. Throws an exception if any input is illegal.
dna-repeated-seqs
(dna-repeated-seqs coord-start coord-end ref ncopy)
Constructor of DNARepeatedSeqs. Throws an exception if any input is illegal.
dna-substitution
(dna-substitution coord ref typ)(dna-substitution coord ref typ alt)
Constructor of DNASubstitution. Throws an exception if any input is illegal.
equiv
(equiv mutation1 mutation2)
long-amino-acids
A list of three-letter amino acids.
Mutation
protocol
members
plain
(plain this)
Returns a plain map representing the given mutation.
parse-dna
(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
(parse-dna-alleles s kind)
parse-dna-conversion
(parse-dna-conversion s kind)
parse-dna-deletion
(parse-dna-deletion s kind)
parse-dna-duplication
(parse-dna-duplication s kind)
parse-dna-indel
(parse-dna-indel s kind)
parse-dna-insertion
(parse-dna-insertion s kind)
parse-dna-inversion
(parse-dna-inversion s kind)
parse-dna-repeated-seqs
(parse-dna-repeated-seqs s kind)
parse-dna-substitution
(parse-dna-substitution s kind)
parse-protein
(parse-protein s)
Parses a protein mutation string s, returning a record implementing Mutation
protocol.
parse-protein-alleles
(parse-protein-alleles s)
parse-protein-deletion
(parse-protein-deletion s)
parse-protein-duplication
(parse-protein-duplication s)
parse-protein-extension
(parse-protein-extension s)
parse-protein-frame-shift
(parse-protein-frame-shift s)
parse-protein-indel
(parse-protein-indel s)
parse-protein-insertion
(parse-protein-insertion s)
parse-protein-repeated-seqs
(parse-protein-repeated-seqs s)
parse-protein-substitution
(parse-protein-substitution s)
parse-rna
(parse-rna s)
Parses a RNA mutation string s, returning a record implementing Mutation
protocol.
parse-rna-alleles
(parse-rna-alleles s)
parse-rna-conversion
(parse-rna-conversion s)
parse-rna-deletion
(parse-rna-deletion s)
parse-rna-duplication
(parse-rna-duplication s)
parse-rna-indel
(parse-rna-indel s)
parse-rna-insertion
(parse-rna-insertion s)
parse-rna-inversion
(parse-rna-inversion s)
parse-rna-repeated-seqs
(parse-rna-repeated-seqs s)
parse-rna-substitution
(parse-rna-substitution s)
parse-uncertain-mutation
(parse-uncertain-mutation s kind)
protein-alleles
(protein-alleles mutations1 mutations2)
protein-deletion
(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
(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
(protein-extension ref coord alt region new-site)
Constructor of ProteinExtension. Throws an exception if any input is illegal.
protein-frame-shift
(protein-frame-shift ref coord alt new-ter-site)
Constructor of ProteinFrameShift. Throws an exception if any input is illegal.
protein-indel
(protein-indel ref-start coord-start ref-end coord-end alts)
Constructor of ProteinIndel. Throws an exception if any input is illegal.
protein-insertion
(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
(protein-no-effect)
protein-repeated-seqs
(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
(protein-substitution ref coord alt)
Constructor of ProteinSubstitution. Throws an exception if any input is illegal.
protein-unknown-mutation
(protein-unknown-mutation)
restore
multimethod
(restore m)
Restores a plain map to a suitable mutation record.
rna-alleles
(rna-alleles mutations1 mutations2)
rna-conversion
(rna-conversion coord-start coord-end alt)
Constructor of RNAConversion. Throws an exception if any input is illegal.
rna-deletion
(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
(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
(rna-indel coord-start coord-end ref alt)
Constructor of RNAIndel. Throws an exception if any input is illegal.
rna-insertion
(rna-insertion coord-start coord-end alt)
Constructor of RNAInsertion. Throws an exception if any input is illegal.
rna-inversion
(rna-inversion coord-start coord-end)
Constructor of RNAInversion. Throws an exception if any input is illegal.
rna-no-effect
(rna-no-effect)
rna-repeated-seqs
(rna-repeated-seqs coord-start coord-end ref ncopy)
Constructor of RNARepeatedSeqs. Throws an exception if any input is illegal.
rna-splice-affected
(rna-splice-affected)
rna-substitution
(rna-substitution coord ref alt)
Constructor of RNASubstitution. Throws an exception if any input is illegal.
rna-unknown-mutation
(rna-unknown-mutation)
short-amino-acids
A list of single-letter amino acids.
uncertain-mutation
(uncertain-mutation mutation)
Constructor of UncertainMutation. Throws an exception if any input is
illegal.