Entry_WriteTo writes an entry to an io.Writer. It specifically writes a JSON representation, NOT an XML representation, of the uniprot data.

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

encodeToBase58 encodes a byte slice to a Base58 string

evaluateLoop evaluates and returns the loop enclosed by (closingFivePrimeIdx, closingThreePrimeIdx) which can be either a `Hairpin` or `MultiLoop`. e

see `EvaluateExteriorStem` for more information

getFeatureSequence takes a feature and location object and returns a sequence string.

getStochasticCodon draws a single weighted codon from the provided RNG, advancing its stream. Optimize uses one RNG for the whole sequence and calls t

****************************************************************************** Aug 10, 2024 Fasta **************************************************

****************************************************************************** Aug 16, 2024 Fastq **************************************************

****************************************************************************** Genbank *************************************************************

Evaluate free energy of a hairpin loop. See `evaluateHairpinLoop()` for more information.

internalLoop calculates the free energy of an internal loop. The first and last bp of both left and right sequences are not themselves parts of the l

Returns the minimum of two ints

Return the struct with the lowest free energy that isn't -inf Args: structures: NucleicAcidStructure being compared Returns the min free energy str

multibranch calculates a multi-branch foldEnergy penalty using a linear formula. From Jaeger, Turner, and Zuker, 1989. Found to be better than logari

optimizeOverhangIteration takes in a sequence and optimally fragments it.

TODO rewrite with proper error handling. parses locus from provided string.

adds `length` `inf`s to the front of a slice

readMultiNth reads a multi Gbk from path and parses N entries into a slice of Genbank structs.

removeComments removes C-style inline comments from a string

save our completed attribute / qualifier string to the current feature useful as a wrap-up step from multiple states

removes all white space in a string

trackbackEnergy add energy to each structure, based on how it's unpairedMinimumFreeEnergyW(start,end) differs from the one after Args: structures: T

var ( if_tetraloops, if_hexaloops, if_triloops []int ) func v_init_tetra_hex_tri(sequence string, seq_length int, if_tetraloops, if_hexaloops, if_tri

wrapString wraps the given string within lim width in characters. Wrapping is currently naive and only happens at white-space. A future version of th

CopyLocation creates deep copy of Location, which supports safe duplication

DNASequence returns a random DNA sequence string of a given length and seed.

DesignPrimersWithOverhangs designs two primers to amplify a target sequence, adding on an overhang to the forward and reverse strand. This overhang ca

DualBarcodesToPrimerSet parsers a list of dual barcodes into a dual barcode primer set.

Evaluate a stem branching off the exterior loop. Given a base pair (i,j) (encoded by `energy_params.BasePairTypeEncodedInt()`), compute the energy co

Compute the energy of a hairpin loop. To evaluate the free energy of a hairpin loop, several parameters have to be known. A general hairpin-loop has

EvaluateStemStructure computes the energy of either a stacking pair, bulge, or interior loop. This function computes the free energy of a loop with th

Export returns a json file of the Rebase database

Extend returns a new alphabet that is the original alphabet extended with a list of symbols.

FindKmers finds kmers indicative of ligation events within fastq sequencing reads. If you need to just search raw sequence and not fastq reads, you ca

ForEachValue iterates over the multimap, once for each value do is a callback that takes and a key and value.

HasFeature to check if features from FeatureNames map are available on the current processor

Header is a parsing primitive that should be used when low-level control is needed. It returns the header of the parser, which is usually parsed prior

Header returns an empty header since UniRef files don't have headers

Header returns the parsed sam header.

MD5All reads all the files in the file tree rooted at root and returns a map from file path to the MD5 sum of the file's contents. If the directory wa

Minimap2 aligns sequences using minimap2 over the command line. Right now, only nanopore (map-ont) is supported. If you need others enabled, please pu

NewFastaParserWithMaxLineLength initiates a new FASTA parser from an io.Reader and a user-given maxLineLength.

NewFastqParserWithMaxLineLength initiates a new FASTQ parser from an io.Reader and a user-given maxLineLength.

NewGenbankParserWithMaxLineLength initiates a new Genbank parser from an io.Reader and a user-given maxLineLength.

NewPileupParserWithMaxLineLength initiates a new Pileup parser from an io.Reader and a user-given maxLineLength.

NewSamParserWithMaxLineLength initiates a new SAM parser from an io.Reader and a user-given maxLineLength.

NewSlow5ParserWithMaxLineLength initiates a new SLOW5 parser from an io.Reader and a user-given maxLineLength.

NewStats returns a new instance of codon statistics (a set of statistics we maintain throughout a translation table's lifetime)

NewStemStructure is a wrapper to create a `StemStructure` and call the functions (`(*StemStructure).setStructureType`) required to initialize the stru

NewSubstitutionMatrix creates a new substitution matrix from two alphabets and a 2D array of scores.

****************************************************************************** Parser higher-level functions ***************************************

NextOverhangs gets a list of possible next overhangs to use for an overhang list, along with their efficiencies. This can be used for more optimal fra

****************************************************************************** May 23 2021 Start of the De Bruijn stuff === Barcode basics === We'r

ParseN returns a countN number of records/reads/lines from the parser.

Pileup generates a pileup file from sam alignments. Specifically, it runs the following commands, with the sam alignments in stdin and the templateFas

****************************************************************************** Jan 01, 2024 Below are some helper functions that I've found are usefu

Rebase returns the rebase database as of Nov 27 2023.

ReverseComplementRNA returns the reversed complement of sequence. It is the equivalent of calling revComplement := Reverse(ComplementRNA(sequence))

penalty for 3' AT ****************************************************************************** End of melting temp penalties section for SantaLucia

Score returns the score of two symbols in the substitution matrix.

Similarity returns the Jaccard similarity between two sketches (number of matching hashes / sketch size)

StoreSequence infers and assigns the value of feature.Sequence if currently an empty string.

****************************************************************************** Aug 15, 2023 StreamVByte (svb) compression of raw signal strength is u