Python compute_offset_to_first_complete_codon Examples

Example #1

def test_compute_offset_to_first_complete_codon_no_trimming():
    # if nothing gets trimmed from the reference sequence, then
    # the offset to the first codon shouldn't change
    eq_(
        compute_offset_to_first_complete_codon(
            offset_to_first_complete_reference_codon=0,
            n_trimmed_from_reference_sequence=0), 0)
    eq_(
        compute_offset_to_first_complete_codon(
            offset_to_first_complete_reference_codon=5,
            n_trimmed_from_reference_sequence=0), 5)

Example #2

def test_compute_offset_to_first_complete_codon_trimming_after_codon():
    # if the number of reference bases trimmed from the reference sequence
    # occurs after the reference codon, then it needs to be rounded up the
    # next multiple of three
    eq_(
        compute_offset_to_first_complete_codon(
            offset_to_first_complete_reference_codon=7,
            n_trimmed_from_reference_sequence=8), 2)
    eq_(
        compute_offset_to_first_complete_codon(
            offset_to_first_complete_reference_codon=7,
            n_trimmed_from_reference_sequence=10), 0)

Example #3

def test_compute_offset_to_first_complete_codon_trimming_before_codon():
    # if the number of reference bases trimmed from the reference sequence
    # occurs before the reference codon, then it should decrease the
    # offset by the amount trimmed
    eq_(
        compute_offset_to_first_complete_codon(
            offset_to_first_complete_reference_codon=7,
            n_trimmed_from_reference_sequence=2), 5)
    eq_(
        compute_offset_to_first_complete_codon(
            offset_to_first_complete_reference_codon=7,
            n_trimmed_from_reference_sequence=7), 0)

Example #4

File: test_variant_sequence_in_reading_frame.py Project: Al3n70rn/isovar

def test_compute_offset_to_first_complete_codon_no_trimming():
    # if nothing gets trimmed from the reference sequence, then
    # the offset to the first codon shouldn't change
    eq_(
        compute_offset_to_first_complete_codon(
            offset_to_first_complete_reference_codon=0,
            n_trimmed_from_reference_sequence=0),
        0)
    eq_(
        compute_offset_to_first_complete_codon(
            offset_to_first_complete_reference_codon=5,
            n_trimmed_from_reference_sequence=0),
        5)

Example #5

File: test_variant_sequence_in_reading_frame.py Project: Al3n70rn/isovar

def test_compute_offset_to_first_complete_codon_trimming_after_codon():
    # if the number of reference bases trimmed from the reference sequence
    # occurs after the reference codon, then it needs to be rounded up the
    # next multiple of three
    eq_(
        compute_offset_to_first_complete_codon(
            offset_to_first_complete_reference_codon=7,
            n_trimmed_from_reference_sequence=8),
        2)
    eq_(
        compute_offset_to_first_complete_codon(
            offset_to_first_complete_reference_codon=7,
            n_trimmed_from_reference_sequence=10),
        0)

Example #6

File: test_variant_sequence_in_reading_frame.py Project: Al3n70rn/isovar

def test_compute_offset_to_first_complete_codon_trimming_before_codon():
    # if the number of reference bases trimmed from the reference sequence
    # occurs before the reference codon, then it should decrease the
    # offset by the amount trimmed
    eq_(
        compute_offset_to_first_complete_codon(
            offset_to_first_complete_reference_codon=7,
            n_trimmed_from_reference_sequence=2),
        5)
    eq_(
        compute_offset_to_first_complete_codon(
            offset_to_first_complete_reference_codon=7,
            n_trimmed_from_reference_sequence=7),
        0)