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61 lines
2.5 KiB
Go
61 lines
2.5 KiB
Go
package obiseq
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import (
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"testing"
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"github.com/stretchr/testify/assert"
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)
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// TestSubsequence tests the Subsequence function.
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//
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// The function tests various cases of the Subsequence method of a BioSequence object.
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// It checks different scenarios of subsequence slicing, including both valid and invalid parameters.
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// The function is designed for unit testing purposes and uses the Go testing package.
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// It asserts that the expected subsequence is returned for each test case and checks for any errors.
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// The function also verifies the correctness of the subsequence qualities, if applicable.
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// The test cases cover both non-circular and circular subsequence slicing.
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// It ensures that the function handles different scenarios such as when `from` is greater than `to`,
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// `from` or `to` is out of bounds, and normal subsequence slicing cases.
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//
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// TestSubsequence does not return any value.
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func TestSubsequence(t *testing.T) {
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// Test case 1: Subsequence with valid parameters and non-circular
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seq := NewBioSequence("ID1", []byte("ATCG"), "")
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sub, err := seq.Subsequence(1, 3, false)
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assert.NoError(t, err)
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assert.Equal(t, []byte("tc"), sub.Sequence())
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seq = NewBioSequenceWithQualities("ID1", []byte("ATCG"), "", []byte{40, 30, 20, 10})
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sub, err = seq.Subsequence(1, 3, false)
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assert.NoError(t, err)
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assert.Equal(t, []byte("tc"), sub.Sequence())
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assert.Equal(t, Quality([]byte{30, 20}), sub.Qualities())
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// Test case 2: Subsequence with valid parameters and circular
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seq2 := NewBioSequence("ID1", []byte("ATCG"), "")
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sub2, err2 := seq2.Subsequence(3, 2, true)
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assert.NoError(t, err2)
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assert.Equal(t, []byte("gat"), sub2.Sequence())
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seq = NewBioSequenceWithQualities("ID1", []byte("ATCG"), "", []byte{40, 30, 20, 10})
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sub, err = seq.Subsequence(3, 2, true)
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assert.NoError(t, err)
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assert.Equal(t, []byte("gat"), sub.Sequence())
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assert.Equal(t, Quality([]byte{10, 40, 30}), sub.Qualities())
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// Test case 3: Subsequence with from greater than to and non-circular
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seq3 := NewBioSequence("ID1", []byte("ATCG"), "")
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_, err3 := seq3.Subsequence(3, 1, false)
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assert.EqualError(t, err3, "from: 3 greater than to: 1")
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// Test case 4: Subsequence with from out of bounds
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seq4 := NewBioSequence("ID1", []byte("ATCG"), "")
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_, err4 := seq4.Subsequence(-1, 2, false)
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assert.EqualError(t, err4, "from out of bounds -1 < 0")
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// Test case 5: Subsequence with to out of bounds
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seq5 := NewBioSequence("ID1", []byte("ATCG"), "")
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_, err5 := seq5.Subsequence(2, 5, false)
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assert.EqualError(t, err5, "to out of bounds 5 > 4")
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}
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