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package

v0.15.5 Latest Latest Go to latest Published: Aug 22, 2021 License: MIT Imports: 5 Imported by: 1

Details

Valid go.mod file
Redistributable license
Tagged version
Stable version
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Repository

github.com/Open-Science-Global/poly

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Documentation ¶

Index ¶

func AddMatchesToSequence(matches []Match, sequence poly.Sequence) poly.Sequence
func AvoidHairpin(stemSize int, hairpinWindow int) func(string) []Match
func ForbiddenSequence(sequencesToRemove []string) func(string) []Match
func GlobalRemoveRepeat(repeatLen int, globalSequence string) func(string) []Match
func MatchSequences(sequences map[string]string) func(string) []Match
func RemoveRepeat(repeatLen int) func(string) []Match
type Match
- func Find(sequence string, finderFunctions []func(string) []Match) []Match

Constants ¶

This section is empty.

Variables ¶

This section is empty.

Functions ¶

func AddMatchesToSequence ¶

func AddMatchesToSequence(matches []Match, sequence poly.Sequence) poly.Sequence

func AvoidHairpin ¶ added in v0.15.5

func AvoidHairpin(stemSize int, hairpinWindow int) func(string) []Match

func ForbiddenSequence ¶

func ForbiddenSequence(sequencesToRemove []string) func(string) []Match

RemoveSequence is a generator for a problematicSequenceFuncs for specific sequences.

func GlobalRemoveRepeat ¶

func GlobalRemoveRepeat(repeatLen int, globalSequence string) func(string) []Match

Example ¶

sequence := "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"
var functions []func(string) []Match
functions = append(functions, GlobalRemoveRepeat(33, "ATGAGTATTCAACATTTCCGTGTCGCCCTTATT"))

problems := Find(sequence, functions)
fmt.Println(problems)

Output:

[{0 33 Global repeated sequence | ATGAGTATTCAACATTTCCGTGTCGCCCTTATT}]

func MatchSequences ¶

func MatchSequences(sequences map[string]string) func(string) []Match

Example ¶

sequence := "AAAAAATCGGTCGTAAGGTCTCAAAATTGAGACC"
var functions []func(string) []Match
functions = append(functions, MatchSequences(map[string]string{"GGTCTC": "BsaI restriction binding site"}))

problems := Find(sequence, functions)
fmt.Println(problems)

Output:

[{16 22 BsaI restriction binding site | GGTCTC} {28 34 BsaI restriction binding site | GAGACC}]

func RemoveRepeat ¶

func RemoveRepeat(repeatLen int) func(string) []Match

RemoveRepeat is a generator to make a problematicSequenceFunc for repeats.

Example ¶

sequence := "AAAAAATCGGTCGTAAGGTCTCAAAATTGAGACC"
var functions []func(string) []Match
functions = append(functions, RemoveRepeat(5))

problems := Find(sequence, functions)
fmt.Println(problems)

Output:

[{1 6 Repeated sequence | AAAAA} {22 27 Repeated sequence | AAAAT}]

Types ¶

type Match ¶

type Match struct {
	Start   int
	End     int
	Message string
}

func Find ¶

func Find(sequence string, finderFunctions []func(string) []Match) []Match

Source Files ¶

View all Source files

finder.go

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