seismicrna.relate.py.tests package

Submodules

class seismicrna.relate.py.tests.cigar_test.TestParseCigar(methodName='runTest')

Bases: TestCase

Test function parse_cigar.

test_cigar_align_valid()

Parse a valid CIGAR string with align codes.

test_cigar_match_subst_valid()

Parse a valid CIGAR string with match and subst codes.

class seismicrna.relate.py.tests.encode_test.TestEncodeMatch(methodName='runTest')

Bases: TestCase

Test function encode_match.

test_encode_match_hi_qual()

Test when the quality is at least the minimum.

test_encode_match_lo_qual()

Test when the quality is less than the minimum.

class seismicrna.relate.py.tests.encode_test.TestEncodeRelate(methodName='runTest')

Bases: TestCase

Test function encode_relate.

test_encode_relate_hi_qual()

Test when the quality is at least the minimum.

test_encode_relate_lo_qual()

Test when the quality is less than the minimum.

class seismicrna.relate.py.tests.relate_test.TestFindRelsLine(methodName='runTest')

Bases: TestCase

Test function relate.relate_line.

iter_cases(refseq: DNA, max_ins: int = 2)

Iterate through every test case.

static relate(ref: str, refseq: DNA, read: DNA, qual: str, cigar: str, end5: int, ambindel: bool, clip_end5: int, clip_end3: int)

Generate a SAM line from the given information, and use it to compute a relation vector.

test_aaaa_0ins()

Test all possible reads with 0 insertions from AAAA.

test_aaaaaa_0ins()

Test all possible reads with 0 insertions from AAAAAA.

test_aacc_1ins()

Test all possible reads with ≤ 1 insertion from AACC.

test_acgt_1ins()

Test all possible reads with ≤ 1 insertion from ACGT.

test_all_matches()

test_ambig_delet_low_qual()

Test ambiguous deletions with all low-quality positions.

test_soft_clips()

class seismicrna.relate.py.tests.relate_test.TestMergeMates(methodName='runTest')

Bases: TestCase

test_both_blank()

test_both_reads()

test_empty()

test_overhangs()

test_read1()

test_read2()