synthesis

package
v0.15.5 Latest Latest
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 Go to latest Published: Aug 22, 2021 License: MIT Imports: 12 Imported by: 0

Documentation

Index

Examples

Constants

This section is empty.

Variables

View Source 
var FixIterations = 100

Functions

func GcContentFixer added in v0.13.5 

func GcContentFixer(upperBound, lowerBound float64) func(string, chan DnaSuggestion, *sync.WaitGroup)

GcContentFixer is a generator to increase or decrease the overall GcContent of a CDS.

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 RemoveHairpin added in v0.13.5 

func RemoveHairpin(stemSize int, hairpinWindow int) func(string, chan DnaSuggestion, *sync.WaitGroup)

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 Change added in v0.13.5 

type Change struct {
	Position int    `db:"position"`
	Step     int    `db:"step"`
	From     string `db:"codonfrom"`
	To       string `db:"codonto"`
	Reason   string `db:"reason"`
}

func FixCds 

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

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"`
}

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

Source Files

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