Synthesis fixer (#98)

* Added manifesto of how and why

* Working a little on the synthesisFixer

* First round of new synthesisFixer with sqlite

* Work in progress

* Work in progress with SQL synthesisFixer

* Passes go test

* Figuring out tests

* FixCds now works with an example

* updates

* Moved synthesis fixer from transformations -> synthesis

* Improved comment for synthesis.go

* Added FindTypeIIS for Pichia work

* Removed overlap loop. It can be buggy and a proper overlap function should be added later.

* Fixed index issue

* Added test case fixing error in sqlFix where NA would not look for GC or AT biases

* 1000 iterations -> 100

* Fix linter issues

* Added generator for naughty sequences

* Added repeat remover

* Added iterations as variable

* Added GcContent function

* Remove intersect

* Added FixCdsSimple example

* refactor synthesis stuff into its own subpackage and update fn calls after `repackage` PR

* update direct dependencies and fn calls to match update

* update `codon.chooser()` err to include source of error

* update copyright year.

* added random.DNASequence function. (#179)

* Updated go.mod to remove dependency on CGO.

* Add example

* Update to synthesis.go

* Added additional docs

* Add comment to sqlite blank import

* Fixed stuff for code climate

* Added concurrent parsing feature for genbank files (#182)

* Added concurrent parsing feature for genbank files

* Added ParseFlatConcurrent

* Updated to have generic CheckSum instead of just MD5

* Tutorials (#184)

* Added example_test for genbank and gff

* Added SIMPLE tutorials and notes for each parser.

* Revamped seqhash docs and added simple tutorial

* moved example seqhash to example_test - does this make it runnable?

Co-authored-by: Timothy Stiles <tim@stiles.io>

* Fixed problem with stop codons

* Added change log and fixed gcbias bug

* Change log now has ordering

* Added change comment string

* Added gc content checker

* Test where the codon choosed by the sql query is actually not with the highest weight

* Create a feature to removes repetitions between cds and a external sequence as host genome or plasmid to avoid homology recombination

* fix linters indications

* Hairpin remover function for FixCds and test

* Fix for checking if we have a full CDS sequence without interrupted codons

* Fix for genbank files exported from benchling that have a different index for slash in qualifiers

* Lint correction

* Synthesis fix for correctly choose the highest synonymous codon

* fixed typo

* Fixed reversion error with DESC statement.

* Fixed linter for synthesisFixer

* Fix error message

* enzymes -> sequencesToRemove

* Changed name of enzymes

* Changed fixiterations

* 100% test coverage with updates

* Changed wg -> waitgroup

* Fix linter issues

* Add better message for failures

* Add comment to synthesis fixer

* Added comments on sql

* codonLength

* Removed kmer table stuff - will add again with kmer table for synthesisFixer

Co-authored-by: Vivek Raja <vivek.r.raja@gmail.com>
Co-authored-by: Tim <TimothyStiles@users.noreply.github.com>
Co-authored-by: Timothy Stiles <tim@stiles.io>
Co-authored-by: Isaac Guerreiro <ig00114@saqueepague.com.br>

Author: 4 people

checks/checks.go

@@ -1,9 +1,21 @@
 package checks
 
-import "github.com/TimothyStiles/poly/transform"
+import (
+	"github.com/TimothyStiles/poly/transform"
+	"strings"
+)
 
 // IsPalindromic accepts a sequence of even length and returns if it is
 // palindromic. More here - https://en.wikipedia.org/wiki/Palindromic_sequence
 func IsPalindromic(sequence string) bool {
 	return sequence == transform.ReverseComplement(sequence)
 }
+
+// GcContent checks the GcContent of a given sequence.
+func GcContent(sequence string) float64 {
+	sequence = strings.ToUpper(sequence)
+	GuanineCount := strings.Count(sequence, "G")
+	CytosineCount := strings.Count(sequence, "C")
+	GuanineAndCytosinePercentage := float64(GuanineCount+CytosineCount) / float64(len(sequence))
+	return GuanineAndCytosinePercentage
+}

checks/checks_test.go

@@ -13,3 +13,10 @@ func TestIsPalindromic(t *testing.T) {
 		t.Errorf("IsPalindromic failed call BsaI NOT a palindrome")
 	}
 }
+
+func TestGcContent(t *testing.T) {
+	content := GcContent("GGTATC")
+	if content != 0.5 {
+		t.Errorf("GcContent did not properly calculate GC content")
+	}
+}