synthesis

package

v0.11.4 Latest Latest Go to latest Published: Aug 2, 2021 License: MIT Imports: 11 Imported by: 0

Details

Valid go.mod file
Redistributable license
Tagged version
Stable version
Learn more about best practices

Repository

github.com/Open-Science-Global/poly

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Documentation ¶

Index ¶

Variables
func FixCds(sqlitePath string, sequence string, codontable codon.Table, ...) (string, error)
func FixCdsSimple(sequence string, codontable codon.Table, sequencesToRemove []string) (string, error)
func GlobalRemoveRepeat(repeatLen int, globalKmers map[string]bool) func(string, chan DnaSuggestion, *sync.WaitGroup)
func RemoveRepeat(repeatLen int) func(string, chan DnaSuggestion, *sync.WaitGroup)
func RemoveSecondaryStructure(closeIndex int) func(string, chan DnaSuggestion, *sync.WaitGroup)
func RemoveSequence(sequencesToRemove []string) func(string, chan DnaSuggestion, *sync.WaitGroup)
type DnaSuggestion

Constants ¶

This section is empty.

Variables ¶

View Source

var FixIterations = 100

Functions ¶

func FixCds ¶

func FixCds(sqlitePath string, sequence string, codontable codon.Table, problematicSequenceFuncs []func(string, chan DnaSuggestion, *sync.WaitGroup)) (string, error)

FixCds fixes a CDS given the CDS sequence, a codon table, and a list of functions to solve for.

Example ¶

bla := "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"
sequence := genbank.Read(dataDir + "ecoli-mg1655.gff")
codonTable := codon.GetCodonTable(11)
codingRegions := codon.GetCodingRegions(sequence)
optimizationTable := codonTable.OptimizeTable(codingRegions)

var functions []func(string, chan DnaSuggestion, *sync.WaitGroup)
functions = append(functions, RemoveSequence([]string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC"}))

fixedSeq, _ := FixCds(":memory:", bla, optimizationTable, functions)
fmt.Println(fixedSeq)

Output:

ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG

func FixCdsSimple ¶

func FixCdsSimple(sequence string, codontable codon.Table, sequencesToRemove []string) (string, error)

FixCdsSimple is FixCds with some defaults for normal usage, including finding homopolymers, finding repeats, and ensuring a normal range of GC content. It also allows users to put in sequences that they do not wish to occur within their CDS, like restriction enzyme cut sites.

Example ¶

bla := "ATGAAAAAAAAAAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"

sequence := genbank.Read(dataDir + "ecoli-mg1655.gff")
codonTable := codon.GetCodonTable(11)
codingRegions := codon.GetCodingRegions(sequence)
optimizationTable := codonTable.OptimizeTable(codingRegions)

fixedSeq, _ := FixCdsSimple(bla, optimizationTable, []string{"GGTCTC"})
fmt.Println(fixedSeq)

Output:

ATGAAGAAAAAAAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG

func GlobalRemoveRepeat ¶ added in v0.11.4

func GlobalRemoveRepeat(repeatLen int, globalKmers map[string]bool) func(string, chan DnaSuggestion, *sync.WaitGroup)

GlobalRemoveRepeat is a generator to make a function that searchs for external repeats (e.g genome repeats) and make a DnaSuggestion for codon changes.

func RemoveRepeat ¶

func RemoveRepeat(repeatLen int) func(string, chan DnaSuggestion, *sync.WaitGroup)

RemoveRepeat is a generator to make a problematicSequenceFunc for repeats.

func RemoveSecondaryStructure ¶ added in v0.11.4

func RemoveSecondaryStructure(closeIndex int) func(string, chan DnaSuggestion, *sync.WaitGroup)

RemoveRepeat is a generator to make a problematicSequenceFunc for repeats.

func RemoveSequence ¶

func RemoveSequence(sequencesToRemove []string) func(string, chan DnaSuggestion, *sync.WaitGroup)

RemoveSequence is a generator for a problematicSequenceFuncs for specific sequences.

Types ¶

type DnaSuggestion ¶

type DnaSuggestion struct {
	Start          int    `db:"start"`
	End            int    `db:"end"`
	Bias           string `db:"gcbias"`
	QuantityFixes  int    `db:"quantityfixes"`
	SuggestionType string `db:"suggestiontype"`
	Step           int    `db:"step"`
	Id             int    `db:"id"`
}

DnaSuggestion is a suggestion of a fixer, generated by a problematicSequenceFunc.

Source Files ¶

View all Source files

synthesis.go

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