This example shows how to use the fragmenter to fragment a gene in preparation for synthesis. Inputs are the sequence, the minimal fragment length, th

This example shows basic usage of the synthesis package. In this example, we will remove BsaI sites from the bla gene, commonly found in pUC plasmids.

This example shows how to design a sequence.

This example shows how to seqhash a sequence.

This example reads rebase into an enzymeMap and returns the AarI recognition sequence.

This example shows how to open a uniprot data dump file and read the results into a list. Directly using the channel without converting to an array sh

This example shows how to open a file with the fasta parser. The sequences within that file can then be analyzed further with different software.

Example_read shows an example of reading a file from disk.

Example_readGz shows an example of reading and parsing a gzipped file.

FilterData is a generic function that implements a channel filter. Users give an input and output channel, with a filtering function, and FilterData f

Fragment fragments a sequence into fragments between the min and max size, choosing fragment ends for optimal assembly efficiency. Since fragments wil

export FragmentSequence

export FragmentSequenceWithOverhangs

GcContent checks the GcContent of a given sequence.

GenerateVCF generates a VCF file from sam alignments. Specifically, it runs the following commands, with sam alignments in stdin and the templateFasta

Get gets a uniprot from its accessionID

GetUniRefVersion returns "50", "90", or "100" based on the XML root element name

GetWeightedAminoAcids returns the amino acids along with their associated codon weights

export GoldenGate

HasExtendedFeature to check if features from ExtendedFeatureNames map are available on the current processor

HasExtraFeature to check if features from ExtraFeatureNames map are available on the current processor

HasThermalAndPowerFeature to check if features from ThermalAndPowerFeatureNames map are available on the current processor

Header returns nil,nil.

Header returns nil,nil.

Header returns nil,nil.

Header returns nil,nil.

Header returns nil,nil.

IsPalindromic accepts a sequence of even length and returns if it is palindromic. More here - https://en.wikipedia.org/wiki/Palindromic_sequence

IsValidDotBracketStructure accepts a string and checks if it uses valid dot-bracket notation. See the `secondary_structure` package for more info on d

IsValidRNA accepts a string and checks if it is a valid RNA sequence.

JSONToMatches converts a JSON string to a slice of Match structs.

export Ligate

ManyToChannel is a generic function that implements the ManyXXXToChannel functions. It properly does concurrent parsing of many parsers to a single ch

MarmurDoty calculates the melting point of an extremely short DNA sequence (<15 bp) using a modified Marmur Doty formula [Marmur J & Doty P (1962). De

MatchesToJSON converts a slice of Match structs to a JSON string.

MeltingTemp calls SantaLucia with default inputs for primer and salt concentration.

Minimap2Channeled uses channels rather than io.Reader and io.Writers.

NeedlemanWunsch performs global alignment between two strings using the Needleman-Wunsch algorithm. It returns the final score and the optimal alignme

New initializes a new mash sketch.

NewEnergyParams is a wrapper function that calls the required functions which parse the specified energy parameter set and scales it by `temperatureIn

NewFastaParser initiates a new FASTA parser from an io.Reader.

NewFastqParser initiates a new FASTQ parser from an io.Reader.

NewGenbankParser initiates a new Genbank parser form an io.Reader.

NewMegamashMap creates a megamash map that can be searched against.

NewPileupParser initiates a new Pileup parser from an io.Reader.

NewSamParser initiates a new SAM parser from an io.Reader.

NewScoring returns a new Scoring struct with default values for DNA.

NewSlow5Parser initiates a new SLOW5 parser from an io.Reader.

NewUniprotParser initiates a new Uniprot parser from an io.Reader. No maxLineLength is necessary.

NewUnirefParser initiates a new Uniref parser from an io.Reader. No maxLineLength is necessary.

NextOverhang gets next most efficient overhang to use for a given set of overhangs. This is useful for when developing a new set of standard overhangs

export NextOverhang

export NextOverhangs

ParseDualPrimerSet parses a csv file into a DualBarcodePrimerSet.

export ParseFastaFromCFile

export ParseFastaFromCString

export ParseFastqFromCFile

export ParseFastqFromCString

export ParseGenbankFromCFile

export ParseGenbankFromCString

PileupChanneled processes SAM alignments from a channel and sends pileup lines to another channel.

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

RecursiveFragment fragments a sequence recursively into an assembly, which can be created from sub-assemblies. This function is for designing large pi

export RecursiveFragmentSequence

RunWorkers starts a specified number of workers, each executing the provided WorkerFunc. It uses an errgroup.Group to manage the workers and handle er

****************************************************************************** Aug 28, 2024 Fragment Package Functions *****************************