seismicrna.core.seq.tests package

Submodules

class seismicrna.core.seq.tests.fasta_test.TestFormat(methodName='runTest')

Bases: TestCase

test_format_fasta_name_line()

test_format_fasta_record()

test_format_fasta_seq_lines()

class seismicrna.core.seq.tests.fasta_test.TestParseFasta(methodName='runTest')

Bases: TestCase

test_duplicate_name()

test_invalid_name()

test_invalid_seq()

test_valid_blank_line()

test_valid_dna()

test_valid_empty()

test_valid_names()

test_valid_rna()

class seismicrna.core.seq.tests.fasta_test.TestValidFastaSeqname(methodName='runTest')

Bases: TestCase

test_blank()

test_illegal_prefix()

test_illegal_suffix()

test_misformatted()

test_name_mark()

test_valid()

class seismicrna.core.seq.tests.fasta_test.TestWriteFasta(methodName='runTest')

Bases: TestCase

test_blank_name()

test_force()

test_invalid_name()

test_valid_names()

class seismicrna.core.seq.tests.region_test.TestConstants(methodName='runTest')

Bases: TestCase

test_base_name()

test_full_name()

test_pos_name()

test_seq_index_names()

class seismicrna.core.seq.tests.region_test.TestGetSharedIndex(methodName='runTest')

Bases: TestCase

Test function get_shared_index.

test_one_invalid()

test_one_valid()

test_two_invalid()

test_two_valid()

test_zero_invalid()

test_zero_valid()

class seismicrna.core.seq.tests.region_test.TestGetWindows(methodName='runTest')

Bases: TestCase

Test function get_windows.

compare(expected: list, *series: Series, **kwargs)

test_1_series_size_1_min_0_excl_nan()

test_1_series_size_1_min_0_incl_nan()

test_1_series_size_1_min_1_excl_nan()

test_1_series_size_1_min_1_incl_nan()

test_1_series_size_2_min_1_excl_nan()

test_1_series_size_2_min_1_incl_nan()

test_1_series_size_2_min_2_excl_nan()

test_1_series_size_2_min_2_incl_nan()

test_2_series_size_1_min_0_excl_nan()

test_2_series_size_1_min_0_incl_nan()

test_2_series_size_1_min_1_excl_nan()

test_2_series_size_1_min_1_incl_nan()

test_2_series_size_2_min_0_excl_nan()

test_2_series_size_2_min_0_incl_nan()

test_2_series_size_2_min_1_excl_nan()

test_2_series_size_2_min_1_incl_nan()

test_2_series_size_2_min_2_excl_nan()

test_2_series_size_2_min_2_incl_nan()

test_empty()

class seismicrna.core.seq.tests.region_test.TestHyphenateEnds(methodName='runTest')

Bases: TestCase

Test function hyphenate_ends.

test_hyphenate()

class seismicrna.core.seq.tests.region_test.TestIndexToPos(methodName='runTest')

Bases: TestCase

Test function index_to_pos.

test_valid_full()

Test with a valid full sequence.

test_valid_noncontig()

Test with non-contiguous sequence.

test_valid_slice()

Test with a valid slice of a sequence.

class seismicrna.core.seq.tests.region_test.TestIndexToSeq(methodName='runTest')

Bases: TestCase

Test function index_to_seq.

test_invalid_noncontig()

Test with non-contiguous sequence, forbidding gaps.

test_valid_empty_seq()

Test with an empty sequence and no positions.

test_valid_full()

Test with a valid full sequence.

test_valid_no_pos()

Test with a valid sequence and no positions.

test_valid_noncontig()

Test with non-contiguous sequence, allowing gaps.

test_valid_slice()

Test with a valid slice of a sequence.

class seismicrna.core.seq.tests.region_test.TestIntersect(methodName='runTest')

Bases: TestCase

test_diff_refs()

test_diff_seqs()

test_empty_invalid()

test_one_full()

test_one_full_named()

test_one_masked()

test_one_slice()

test_three_overlapping()

test_two_disjoint()

test_two_full()

test_two_masked()

test_two_overlapping()

class seismicrna.core.seq.tests.region_test.TestRegionAddMask(methodName='runTest')

Bases: TestCase

test_add_mask()

test_add_mask_complement()

test_add_mask_invalid()

test_add_overlapping_masks()

test_add_unordered_mask()

test_update_mask()

test_update_mask_complement()

class seismicrna.core.seq.tests.region_test.TestRegionCopy(methodName='runTest')

Bases: TestCase

test_copy()

class seismicrna.core.seq.tests.region_test.TestRegionEqual(methodName='runTest')

Bases: TestCase

test_diff_end3()

test_diff_end5()

test_diff_full()

test_diff_mask_name()

test_diff_mask_positions()

test_diff_name()

test_diff_ref()

test_diff_seq()

test_diff_seq5()

test_equal_full()

test_equal_mask()

test_equal_part()

class seismicrna.core.seq.tests.region_test.TestRegionInit(methodName='runTest')

Bases: TestCase

test_full()

Create a region from a full reference sequence.

test_full_blank_name()

Create a region with a hyphenated name from a full reference sequence.

test_full_end3()

Create a region with a hyphenated name from a full reference sequence.

test_full_end5()

Create a region with a hyphenated name from a full reference sequence.

test_full_given_name()

Create a region with a given name from a full reference sequence.

test_partial_reflen_equal()

Create a region from part of a reference sequence.

test_partial_reflen_greater()

Create a region from part of a reference sequence.

test_partial_reflen_less()

Create a region from part of a reference sequence.

test_partial_seq5_equal()

Create a region from part of a reference sequence.

test_partial_seq5_greater()

Create a region from part of a reference sequence.

test_partial_seq5_less()

Create a region from part of a reference sequence.

test_partial_seq5_reflen()

Create a region from part of a reference sequence.

test_partial_slice()

Region from part of a slice of a reference sequence.

test_partial_slice_invalid_end3()

Region from part of a slice of a reference sequence.

test_partial_slice_invalid_end5()

Region from part of a slice of a reference sequence.

test_partial_slice_invalid_reflen()

Region from part of a slice of a reference sequence.

test_partial_slice_invalid_seq5()

Region from part of a slice of a reference sequence.

test_slice_end3_equal()

Create a region from a slice of a reference sequence.

test_slice_end3_greater()

Create a region from a slice of a reference sequence.

test_slice_end3_less()

Create a region from a slice of a reference sequence.

test_slice_end5_end3()

Create a region from a slice of a reference sequence.

test_slice_end5_end3_invalid()

Create a region from a slice of a reference sequence.

test_slice_end5_equal()

Create a region from a slice of a reference sequence.

test_slice_end5_greater()

Create a region from a slice of a reference sequence.

test_slice_end5_less()

Create a region from a slice of a reference sequence.

class seismicrna.core.seq.tests.region_test.TestRegionLength(methodName='runTest')

Bases: TestCase

test_full_lengths()

test_partial_lengths()

test_slice_lengths()

class seismicrna.core.seq.tests.region_test.TestRegionMaskGU(methodName='runTest')

Bases: TestCase

test_find_gu()

test_mask_gu()

class seismicrna.core.seq.tests.region_test.TestRegionMaskList(methodName='runTest')

Bases: TestCase

test_mask_list()

class seismicrna.core.seq.tests.region_test.TestRegionMaskNames(methodName='runTest')

Bases: TestCase

test_get_mask()

test_mask_names()

class seismicrna.core.seq.tests.region_test.TestRegionMaskPolyA(methodName='runTest')

Bases: TestCase

test_find_polya()

test_mask_polya()

class seismicrna.core.seq.tests.region_test.TestRegionMasked(methodName='runTest')

Bases: TestCase

test_masked_bool()

test_masked_int()

test_masked_zero()

class seismicrna.core.seq.tests.region_test.TestRegionRange(methodName='runTest')

Bases: TestCase

test_range()

test_range_int()

test_range_one()

class seismicrna.core.seq.tests.region_test.TestRegionUnmasked(methodName='runTest')

Bases: TestCase

test_size()

test_unmasked()

test_unmasked_bool()

test_unmasked_int()

test_unmasked_zero()

class seismicrna.core.seq.tests.region_test.TestSeqPosToIndex(methodName='runTest')

Bases: TestCase

Test function seq_pos_to_index.

test_invalid_dup_1()

Test with duplicated positions, starting at 1.

test_invalid_empty_seq_1()

Test with an empty sequence and start position 0.

test_invalid_empty_seq_2()

Test with an empty sequence and position 0.

test_invalid_empty_seq_3()

Test with an empty sequence and one position.

test_invalid_full_0()

Test with every position in the sequence, starting at 0.

test_invalid_greater_end_9()

Test with a position greater than end, starting at 9.

test_invalid_less_start_2()

Test with a position less than start (= 2).

test_invalid_unsort_1()

Test with unsorted positions, starting at 1.

test_valid_empty_1()

Test with no positions, starting at 1.

test_valid_empty_seq()

Test with an empty sequence and no positions.

test_valid_full_1()

Test with every position in the sequence, starting at 1.

test_valid_full_9()

Test with every position in the sequence, starting at 9.

test_valid_noncontig_2()

Test with non-contiguous sequence, starting at 2.

test_valid_slice_6()

Test with a slice of the sequence, starting at 6.

class seismicrna.core.seq.tests.region_test.TestSubregion(methodName='runTest')

Bases: TestCase

test_full_region_full_length_sub()

test_full_region_full_sub()

test_full_region_full_sub_end3()

test_full_region_full_sub_end5()

test_full_region_full_sub_name()

test_partial_trunc_region_trunc_sub()

test_trunc_region_full_sub()

test_trunc_region_trunc_sub()

class seismicrna.core.seq.tests.region_test.TestUnite(methodName='runTest')

Bases: TestCase

test_diff_refs()

test_diff_seqs()

test_empty_invalid()

test_one_full()

test_one_full_named()

test_one_masked()

test_one_slice()

test_two_disjoint()

test_two_disjoint_refseq()

test_two_disjoint_wrong_refseq()

test_two_full()

test_two_masked()

test_two_overlapping()

test_two_overlapping_refseq()

class seismicrna.core.seq.tests.region_test.TestWindowToMargins(methodName='runTest')

Bases: TestCase

Test function window_to_margins.

test_window_0()

test_window_float()

test_window_length()

test_window_margins()

Tests for Sequence Core Module.

---

class seismicrna.core.seq.tests.xna_test.TestDNA(methodName='runTest')

Bases: TestCase

Test class DNA.

test_alph()

test_bool()

Test that only zero-length DNA sequences are falsy.

test_contains()

test_get_alphaset()

test_get_comp()

test_get_comptrans()

test_get_nonalphaset()

test_invalid_bases()

Test whether invalid characters raise ValueError.

test_kmers()

test_picto()

Test pictograms.

test_random()

Test whether random DNA sequences can be created.

test_reverse_complement()

Test reverse complementing DNA sequences.

test_slice()

Test slicing DNA sequences.

test_to_array()

Test generating NumPy arrays from DNA sequences.

test_transcribe()

Test transcribing DNA sequences.

test_valid()

Test whether valid DNA sequences can be created.

class seismicrna.core.seq.tests.xna_test.TestExpandDegenerateSeq(methodName='runTest')

Bases: TestCase

Test function expand_degenerate_seq.

test_one_degenerate()

Test that one sequence is returned for each DNA base.

test_two_degenerate()

Test that one sequence is returned for every combination of two DNA bases.

test_zero_degenerate()

Test that the original sequence is returned.

class seismicrna.core.seq.tests.xna_test.TestRNA(methodName='runTest')

Bases: TestCase

Test class RNA.

test_alph()

test_bool()

Test that only zero-length RNA sequences are falsy.

test_get_alphaset()

test_get_comp()

test_get_comptrans()

test_get_nonalphaset()

test_invalid_bases()

Test whether invalid characters raise ValueError.

test_picto()

Test pictograms.

test_random()

Test whether random RNA sequences can be created.

test_reverse_complement()

Test reverse complementing RNA sequences.

test_reverse_transcribe()

Test reverse transcribing RNA sequences.

test_slice()

Test slicing RNA sequences.

test_to_array()

Test generating NumPy arrays from RNA sequences.

test_valid()

Test whether valid RNA sequences can be created.

class seismicrna.core.seq.tests.xna_test.TestXNA(methodName='runTest')

Bases: TestCase

Test basic properties of the XNA abstract base class.

test_abstract_base_class()

Test that instantiating an XNA raises a TypeError.

test_dict_str_dna_rna()

Test that instances of str, DNA, and RNA with identical sequences can all be used together as dict keys.

test_equal_dna_dna()

Test that DNA instances with the same sequences compare as equal.

test_equal_rna_rna()

Test that RNA instances with the same sequences compare as equal.

test_hashable_dna()

Test that DNA instances are hashable.

test_hashable_rna()

Test that RNA instances are hashable.

test_not_equal_dna_rna()

Test that DNA and RNA instances with the same sequences compare as not equal.

test_not_equal_dna_str()

Test that DNA and str instances with the same sequences compare as not equal.

test_not_equal_rna_str()

Test that RNA and str instances with the same sequences compare as not equal.

test_set_str_dna_rna()

Test that instances of str, DNA, and RNA with identical sequences can all be used together in a set.