/******************************************************************************

Synthesis Fixer tests begin here

Generally, we are taking tests previously used in DnaChisel along with a few of
our own tests.

https://github.com/Edinburgh-Genome-Foundry/DnaChisel/tree/master/tests/builtin_specifications

The following tests are built into DnaChisel:

- test_AllowPrimer
- test_AvoidBlastMatches
- test_AvoidChanges
- test_AvoidHairpins
- test_AvoidMatches
- test_AvoidRareCodons
- test_AvoidStopCodons
- test_CodonOptimize
- test_EnforceChanges
- test_EnforceChoice
- test_EnforceGCContent
- test_EnforcePatternOccurence
- test_EnforceRegionsCompatibility
- test_EnforceSequence
- test_EnforceTerminalGCContent
- test_EnforceTranslation
- test_SequenceLengthBounds
- test_UniquifyAllKmers




******************************************************************************/
Synthesis Fixer tests begin here

Generally, we are taking tests previously used in DnaChisel along with a few of
our own tests.

github.com/Edinburgh-Genome-Foundry/DnaChisel/tree/master/tests/builtin_specifications

The following tests are built into DnaChisel.


/ ****************************************************************************** Synthesis Fixer tests begin here Generally we are taking tests previously used in DnaChisel along with a few of our own tests . https : // github . com / Edinburgh - Genome - Foundry / DnaChisel / tree / master / tests / builtin_specifications The following tests are built into DnaChisel : - test_AllowPrimer - test_AvoidBlastMatches - test_AvoidChanges - test_AvoidHairpins - test_AvoidMatches - test_AvoidRareCodons - test_AvoidStopCodons - test_CodonOptimize - test_EnforceChanges - test_EnforceChoice - test_EnforceGCContent - test_EnforcePatternOccurence - test_EnforceRegionsCompatibility - test_EnforceSequence - test_EnforceTerminalGCContent - test_EnforceTranslation - test_SequenceLengthBounds - test_UniquifyAllKmers ****************************************************************************** /
func ExampleFixCds() {
	bla := "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA"
	sequence := ReadGbk("data/ecoli-mg1655.gff")
	codonTable := GetCodonTable(11)
	optimizationTable := sequence.GetOptimizationTable(codonTable)
	var functions []func(string, chan DnaSuggestion, *sync.WaitGroup)
	functions = append(functions, FindTypeIIS)
	fixedSeq, _ := FixCds(":memory:", bla, optimizationTable, functions)
	fmt.Println(fixedSeq)
}
func ExampleFixCds ( ) { bla := " " sequence := ReadGbk ( " " ) codonTable := GetCodonTable ( 11 ) optimizationTable := sequence . GetOptimizationTable ( codonTable ) var functions [ ] func ( string , chan DnaSuggestion , * sync . WaitGroup ) functions = append ( functions , FindTypeIIS ) fixedSeq , _ := FixCds ( " " , bla , optimizationTable , functions ) fmt . Println ( fixedSeq ) }
Synthesis Fixer tests begin here
Synthesis Fixer tests begin here
//functions = append(functions, FindBsaI) // Output: ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG