***************************************************************************** Section: Parsing Into Matrices The following section contains funcs nee

Wait blocks until all function calls from the Go method have returned, then returns the first non-nil error (if any) from them.

****************************************************************************** Oct, 15, 2020 Codon table generation stuff begins here. Alright, I kn

Go calls the given function in a new goroutine. It blocks until the new goroutine can be added without the number of active goroutines in the group ex

Parse returns all records/reads/lines from the parser, but does not include the header. It can only be called once on a given parser because it will r

****************************************************************************** GBK specific IO related things end here. ****************************

rescaleDgMatrix maps the function `rescaleDg` onto a given `energy` and `enthalpy` matrix, and returns a matrix with the scaled energy param values (w

NewTranslationTable takes the index of desired NCBI codon table and returns it.

Find the free energy given delta h, s and temp Args: enthalpyHDifference: The enthalpy increment in kcal / mol entropySDifference: The entropy incr

Error returns the error message for AlphabetError.

buildMetaString is a helper function to build the meta section of genbank files.

UpdateWeightsWithSequence will look at the coding regions in the given genbank data, and use those to generate new weights for the codons in the trans

stack returns the free energy of a stack. Using the indexes start and end, check whether it's at the end of the sequence or internal. Then check whet

* # For developers FixCDS is the core function of the synthesis fixing package. It takes a CDS and uses degenerate codons to fix up places with undes

Hash2 creates a version 2 seqhash.

Optimize will return a set of codons which can be used to encode the given amino acid sequence. The codons picked are weighted according to the comput

newFoldingContext returns a context ready to use, in case of error the returned FoldingContext is empty.

EncodeHash2 encodes Hash2 as a base58 string. It also adds a single letter metadata tag that can be used as an easy heuristic for an LLM to identify m

Equal returns true if two nucleicAcidStructures are equal

NewParser parsers a slow5 file.

Sketch generates a mash sketch of the sequence.

WriteTo is a blank function, needed for compatibility with bio parsers. It doesn't do anything.

pair Returns a stack representation, a key for the nearestNeighbors maps Args: s: Sequence being folded start: leftmost index rightOfStart: index

unpairedMinimumFreeEnergyW returns the minimum free energy of a subsequence at start and terminating at end. From Zuker and Stiegler, 1981: let W(i,j

Encode returns the index of a symbol in the alphabet.

SecondaryStructureFromDotBracket returns the annotated structure and `SecondaryStructure` of a RNA sequence from its 'dot-bracket' structure.

WriteTo writes a SAM header to an io.Writer.

returns a slice of length `length` with all values set to `value`

Rescale Gibbs free energy according to the equation dG = dH - T * dS where dG is the change in Gibbs free energy dH is the change in enthalpy dS is

Distance returns the Jaccard distance between two sketches (1 - similarity)

GetSequence returns the sequence of a feature.

Next parses the next read from a parser.

Next reads next fasta genome in underlying reader and returns the result and the amount of bytes read during the call. Next only returns an error if i

CdsSimple is FixCds with some defaults for normal usage, including removing of homopolymers, removing any repeat larger than 18 base pairs, and fixing

****************************************************************************** Base cloning functions begin here. **********************************

Get 0-based ith uint32

RemoveSequence is a generator for a problematicSequenceFuncs for specific sequences.

TryGo calls the given function in a new goroutine only if the number of active goroutines in the group is currently below the configured limit. The r

encodedBasePairType encodes a base pair according to `energy_params.BasePairTypeEncodedInt`

readLine reads a line and returns the line and whether a line could be read

NewParser creates a parser from an io.Reader for pileup data.

NewParser returns a Parser that uses r as the source from which to parse fasta formatted sequences.

Next returns the next Entry from the UniRef file

Next parses the next pileup row in a pileup file. Next returns an EOF if encountered.

Simulate simulates a PCR reaction, including concatemerization analysis. It takes in a list of sequences and list of primers, produces all possible PC

Uint32Encode encode []uint32 with stream vbytes codec as LittleEndian

Zuker folds the DNA sequence and return the lowest free energy score. Based on the approach described in: Zuker and Stiegler, 1981 https://www.ncbi.n

only used for ViennaRNA fold model

ComplementBase accepts a base pair and returns its complement base pair. See Complement. This function expects byte characters in the range a-z and A

DecodeHash2 decodes a seqhash into a [16]byte, including the metadata tag.

Next reads next fastq genome in underlying reader and returns the result and the amount of bytes read during the call. Next only returns an error if i

RotateSequence rotates circular sequences to deterministic point.

Valid returns true if the NucleicAcidStructure is valid

getIntMatrixDims returns the dimensions of a int matrix (up to 6 dimensions)

AllVariantsIUPAC takes a string as input and returns all iupac variants as output

ComplementBaseRNA accepts a RNA base pair and returns its complement base pair. See Complement. This function expects byte characters in the range a-

CutWithEnzyme cuts a given sequence with an enzyme represented by an Enzyme struct. If there is methylated parts of the target DNA, set the "methylate

DotBracket returns the dot-bracket notation of the secondary nucleic acid structure resulting from folding a sequence. Dot-bracket notation, consisti

Compute the energy contribution of a multi-loop stem. Given a base pair (i,j) (encoded by `energy_params.EncodeBasePair()`), compute the energy contr

Ligate simulates ligations. It assumes that fragments can only be ligated in a single way (no 2 fragments with the same overhangs), and also assumes t

Match matches a sequence to all the sequences in a megamash map.

MinimumFreeEnergy return just the delta G of the structures resulting from folding a sequence. Returns the minimum free energy of the folded sequence