Seqfold (#295)

* feat: add seqfold

Add seqfold package, Go port of the python project at:
https://github.com/Lattice-Automation/seqfold

Add general useful types and maps of energies used to calculate the
folding structures.

Add to checks/checks.go a couple of function to determine if a sequence
is DNA or RNA. This is need by `seqfold` to discriminate for example the
energies used in the folding.

* feat: add seqfold functions

Add the functions to calculate the folding energies, the `Fold` function
is the core function to calculate the folding structures and energies of
a nucleotide sequence. The result can be use to print more informations,
e.g. dot-bracket notation of the folded sequence.

* feat: add seqfolg tests and example

Add the unit tests ported from the python codebase and a small example.

* renamed seqfold to fold.

* renamed FoldEnergy to MinimumFreeEnergy.

* renamed s to structure in most of fold.go.

* renamed DNA and RNA energy constants.

* renamed fc to foldContext

* renamed H and S in energies to EnthalpyH and EntropyS.

* changed NN to nearest neighbors.

* renamed BP energy to Matching Basepair energy and s to structure.

* more variable renaming.

* renamed V and W.

* renamed V and W and fixed errors...

* fixed all underscored names in fold_test.go and moved to fold package.

* fixed accidentally modified rebase test data.

* made most function private.

* more public to private functions and structs

* random: add random.RNASequence

* transform: add RNA specific transformations

* fold: use the transform package for complement

And some cleanup

* added minimal biological context and package level comments.

* fold: add fold.Result, un-export most of lib

Add `fold.Resutl` to hold the result of fold.Fold and move there as
methods `MinimumFreeEnergy()` and `DotBracket()`.
In this way we can keep the API surface small without compromising the
package functionality, more methods can be added to `fold.Result` in
case we need them, e.g. `result.JSON()` to obtain a representation of the
resulting structure in JSON or other formats.

* fold: move 1600 magic number in a `const`

Add some explanation as well.

* fold: move the 30 magic number to a const

Add a small explanation as well.

* fold: rename variables

Rename some variables in `unpairedMinimumFreeEnergyW()`

* fold: move magic number 4 in a const

It seem to be used as a minimum length for which stable nucleotide
structures can be made.

* fold: more variable renaming and cleanup

* fold: more var and const rename and refactor

* fold: more renaming

* fold: more magic numbers lifted in constant

* changed fold.Fold to fold.Zuker.

* changed ExampleFold to ExampleZuker.

---------

Co-authored-by: Timothy Stiles <[email protected]>
Co-authored-by: Tim <[email protected]>

checks/checks.go

@@ -23,3 +23,27 @@ func GcContent(sequence string) float64 {
 	GuanineAndCytosinePercentage := float64(GuanineCount+CytosineCount) / float64(len(sequence))
 	return GuanineAndCytosinePercentage
 }
+
+func IsDNA(seq string) bool {
+	for _, base := range seq {
+		switch base {
+		case 'A', 'C', 'T', 'G':
+			continue
+		default:
+			return false
+		}
+	}
+	return true
+}
+
+func IsRNA(seq string) bool {
+	for _, base := range seq {
+		switch base {
+		case 'A', 'C', 'U', 'G':
+			continue
+		default:
+			return false
+		}
+	}
+	return true
+}

checks/checks_test.go

@@ -24,3 +24,65 @@ func TestGcContent(t *testing.T) {
 		t.Errorf("GcContent did not properly calculate GC content")
 	}
 }
+
+func TestIsDNA(t *testing.T) {
+	tests := []struct {
+		name string
+		args string
+		want bool
+	}{
+		{
+			name: "Success",
+			args: "GATTACA",
+			want: true,
+		},
+		{
+			name: "FailRNA",
+			args: "GAUUACA",
+			want: false,
+		},
+		{
+			name: "FailUnknown",
+			args: "RANDOM STRING",
+			want: false,
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if got := checks.IsDNA(tt.args); got != tt.want {
+				t.Errorf("IsDNA() = %v, want %v", got, tt.want)
+			}
+		})
+	}
+}
+
+func TestIsRNA(t *testing.T) {
+	tests := []struct {
+		name string
+		args string
+		want bool
+	}{
+		{
+			name: "Success",
+			args: "GAUUACA",
+			want: true,
+		},
+		{
+			name: "FailDNA",
+			args: "GATTACA",
+			want: false,
+		},
+		{
+			name: "FailUnknown",
+			args: "RANDOM STRING",
+			want: false,
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if got := checks.IsRNA(tt.args); got != tt.want {
+				t.Errorf("IsRNA() = %v, want %v", got, tt.want)
+			}
+		})
+	}
+}