parser

func AssemblyFromCsv ¶

func AssemblyFromCsv(designfile string, partsfile string) (assemblyparameters []enzymes.Assemblyparameters, err error)

func Build_rebase ¶

func Build_rebase(name string, prototype string, recognitionseq string, methylationsite string, commercialsource string, refs string) (Record wtype.RestrictionEnzyme)

func Handlesnapgenelines ¶

func Handlesnapgenelines(lines []string) (dnaseq string)

func MakePartsFromXLSXPartsList ¶

func MakePartsFromXLSXPartsList(data []byte) (parts []*wtype.Liquid, concMap map[string]wunit.Concentration, err error)

MakePartsFromXLSXPartsList parses the parts in an xlsx format design file into a list of LHComponents. The concentration will be set if a concentration column is present in the parts list. If no concentrations are found the parts list will be created with no concentrations and an error returned.

func Parse ¶

func Parse(filename string) (parts_list []string, err error)

func ParseExcel ¶

func ParseExcel(filename string) ([]enzymes.Assemblyparameters, error)

func ParseExcelBinary ¶

func ParseExcelBinary(data []byte) ([]enzymes.Assemblyparameters, error)

ParseExcelBinary parses the contents of a typeIIs assembly design file in xlsx format. An example file is provided: "Assembly_Input_Controls.xlsx" The output will be []enzymes.AssemblyParameters which can be used in the enzymes.Assemblysimulator() and enzymes.Digestionsimulator() functions. The design file is expected to follow a format as shown in the provided example files An error will be returned if no data is found within the .xlsx design file or if the file is not in the expected format.

func ParseGDX ¶

func ParseGDX(file wtype.File) ([]enzymes.Assemblyparameters, error)

ParsesGDX parses a typeIIs assembly design file in gdx format. An example file is provided: "Assembly_Input_Controls.gdx" The output will be []enzymes.AssemblyParameters which can be used in the enzymes.Assemblysimulator() and enzymes.Digestionsimulator() functions. The design file is expected to follow a format as shown in the provided example files An error will be returned if no data is found within the .gdx design file or if the file is not in the expected format.

func ParseGDXBinary ¶

func ParseGDXBinary(data []byte) ([]enzymes.Assemblyparameters, error)

ParseGDXBinary parses the contents of a typeIIs assembly design file in gdx format. An example file is provided: "Assembly_Input_Controls.gdx" The output will be []enzymes.AssemblyParameters which can be used in the enzymes.Assemblysimulator() and enzymes.Digestionsimulator() functions. The design file is expected to follow a format as shown in the provided example files An error will be returned if no data is found within the .gdx design file or if the file is not in the expected format.

func ParsePCRExcel ¶

func ParsePCRExcel(designfile wtype.File) ([]pcr.Reaction, error)

ParsePCRExc3el takes in a pcr design file (.xlsx or .csv) and converts this into an array of type PCRReactions.

func ParseToAssemblyParameters ¶

func ParseToAssemblyParameters(filename string) ([]enzymes.Assemblyparameters, error)

func ReadDesign ¶

func ReadDesign(filename string) [][]string

func ReadParts ¶

func ReadParts(filename string) map[string]wtype.DNASequence

func RebaseParse ¶

func RebaseParse(rebaseRh io.Reader) []wtype.RestrictionEnzyme

func RecognitionSeqHandler ¶

func RecognitionSeqHandler(RecognitionSeq string) (RecognitionSequence string, EndLength int, Topstrand3primedistancefromend int, Bottomstrand5primedistancefromend int, Class string)

func SnapGenetoSimpleSeq ¶

func SnapGenetoSimpleSeq(filename string) (string, error)

func Xlsxparser ¶

func Xlsxparser(filename string, sheetIndex int, outputprefix string) (f *os.File, err error)