seismicrna.relate.tests package
Submodules
- class seismicrna.relate.tests.io_test.TestFromReads(methodName='runTest')
Bases:
TestCase- test_from_0_reads()
- test_from_1_read_0_segs_drop_empty()
- test_from_1_read_0_segs_keep_empty()
- test_from_1_read_1_segs_no_cover_drop_empty()
- test_from_1_read_1_segs_no_cover_keep_empty()
- test_from_1_read_1_segs_no_muts()
- test_from_2_reads_1_2_segs()
- test_from_2_reads_1_segs()
- test_from_2_reads_2_1_segs()
- test_from_2_reads_2_segs()
- test_from_4_reads_varied_segs_drop_empty()
- test_from_4_reads_varied_segs_keep_empty()
- class seismicrna.relate.tests.main_test.TestRelate(*args, **kwargs)
Bases:
TestCase,ABC- batches(min_reads: int = 0, min_mapq: int = 0, min_phred: int = 0, clip_end5: int = 0, clip_end3: int = 0, **kwargs)
- setUp()
Hook method for setting up the test fixture before exercising it.
- tearDown()
Hook method for deconstructing the test fixture after testing it.
- class seismicrna.relate.tests.main_test.TestRelateEmpty(*args, **kwargs)
Bases:
TestRelate- classmethod get_sam_data()
Data for the SAM file.
- test_min_reads()
- test_noargs()
- class seismicrna.relate.tests.main_test.TestRelatePaired(*args, **kwargs)
Bases:
TestRelate- classmethod get_sam_data()
Data for the SAM file.
- test_batch_size_1()
- test_batch_size_4()
- test_batch_size_5()
- test_batch_size_6()
- test_clip()
- test_min_phred()
- test_min_reads()
- test_noargs()
- class seismicrna.relate.tests.main_test.TestRelateSingle(*args, **kwargs)
Bases:
TestRelate- classmethod get_sam_data()
Data for the SAM file.
- test_batch_size_1()
- test_batch_size_3()
- test_clip()
- test_min_phred()
- test_min_reads()
- test_noargs()
- seismicrna.relate.tests.main_test.extract_batches(batches: Iterable[RegionMutsBatch])
- class seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired(methodName='runTest')
Bases:
TestCase- evaluate(expect_ends1: list[tuple[int, int]], expect_ends2: list[tuple[int, int]], expect_rels: dict[int, int], ref: str, refseq: DNA, read1: DNA, qual1: str, cigar1: str, end51: int, read2: DNA, qual2: str, cigar2: str, end52: int)
- relate(ref: str, refseq: DNA, read1: DNA, qual1: str, cigar1: str, end51: int, read2: DNA, qual2: str, cigar2: str, end52: int, ambindel: bool = True, insert3: bool = True, clip_end5: int = 0, clip_end3: int = 0, read1rev: bool = False)
Generate a SAM line from the given information, and use it to compute the relationships.
- relate_error(error_msg: str, ref: str = 'ref', refseq: DNA = DNA('ACGT'), name1: str = 'read', ref1: str = 'ref', cigar1: str = '4M', flag1: int = 83, end51: int = 1, read1: DNA = DNA('ACGT'), qual1: str = 'FFFF', name2: str = 'read', ref2: str = 'ref', flag2: int = 163, end52: int = 1, cigar2: str = '4M', read2: DNA = DNA('ACGT'), qual2: str = 'FFFF', insert3: bool = True, ambindel: bool = True, clip_end5: int = 0, clip_end3: int = 0)
- test_abut()
Reads abut.
R1 GTGC R2 TCGT Ref AGTCAACGT Pos 123456789
- test_abut_int()
Spliced reads abut.
R1 G-GC R2 TC-T Ref AGTCAACGT Pos 123456789
- test_contain()
One read contains the other, with neither end flush.
R1 TgcAT R2 gtaAACG Ref AGTCAACGT Pos 123456789
- test_contain_con_int()
One read contains the other, with neither end flush and a consistent intron.
R1 Tgc_T R2 gtaA_CG Ref AGTCAACGT Pos 123456789
- test_contain_flush3()
One read contains the other, with 3’ ends flush.
R1 TAtCa R2 CggAtCc Ref AGTCAACGT Pos 123456789
- test_contain_flush3_con_int()
One read contains the other, with 3’ ends flush and a consistent intron.
R1 TAt_a R2 CggAt_c Ref AGTCAACGT Pos 123456789
- test_contain_flush3_inc_int()
One read contains the other, with 3’ ends flush and an inconsistent intron.
R1 TAt_a R2 CggAtCc Ref AGTCAACGT Pos 123456789
- test_contain_flush5()
One read contains the other, with 5’ ends flush.
R1 ATcAggG R2 gTcaT Ref AGTCAACGT Pos 123456789
- test_contain_flush53()
Both reads start and end at the same positions.
R1 tc-ACG R2 gGATCG Ref AGTCAACGT Pos 123456789
- test_contain_flush53_con_int()
Both reads start and end at the same positions with a consistent intron.
R1 tc-A_G R2 gGAT_G Ref AGTCAACGT Pos 123456789
- test_contain_flush53_inc_int()
Both reads start and end at the same positions with an inconsistent intron.
R1 tc-A_G R2 g_ATCG Ref AGTCAACGT Pos 123456789
- test_contain_flush5_con_int()
One spliced read contains the other, with 5’ ends flush and a consistent intron.
R1 A_cAggG R2 g_caT Ref AGTCAACGT Pos 123456789
- test_contain_flush5_inc_int()
One spliced read contains the other, with 5’ ends flush and an inconsistent intron.
R1 A_cAggG R2 gT_aT Ref AGTCAACGT Pos 123456789
- test_contain_inc_int()
One read contains the other, with neither end flush and an inconsistent intron.
R1 Tgc_T R2 gtaA__G Ref AGTCAACGT Pos 123456789
- test_diff_names()
- test_gap()
Reads are separated by a gap.
R1 AGTG R2 TCGT Ref AGTCAACGT Pos 123456789
- test_gap_int()
Spliced reads are separated by a gap.
R1 AG-G R2 TC-T Ref AGTCAACGT Pos 123456789
- test_improper()
- test_read_marks()
- test_read_orientation()
- test_staggered()
Reads overlap in a staggered manner.
R1 aGTGgtA R2 AGATGc Ref AGTCAACGT Pos 123456789
- test_staggered_con_int()
Spliced reads overlap in a staggered manner with a consistent intron.
R1 aGT_gtA R2 A_ATGc Ref AGTCAACGT Pos 123456789
- test_staggered_inc_int()
Spliced reads overlap in a staggered manner with an inconsistent intron.
R1 aGT_gtA R2 AGA_Gc Ref AGTCAACGT Pos 123456789
- test_unpaired()
- class seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle(methodName='runTest')
Bases:
TestCase- iter_cases_insert3(refseq: DNA, max_ins: int, insert3: bool, paired: bool)
Iterate through every test case.
- relate(ref: str, refseq: DNA, read: DNA, qual: str, cigar: str, end5: int, insert3: bool, ambindel: bool, clip_end5: int, clip_end3: int, paired: bool = False)
Generate a SAM line from the given information, and use it to compute the relationships.
- relate_error(error_msg: str, error_msg_py: str = '', ref: str = 'ref', refseq: DNA = DNA('ACGT'), read: DNA = DNA('ACGT'), qual: str = 'FFFF', cigar: str = '4M', end5: Any = 1, sam_ref: str = '', mapq: Any = None, flag: Any = None, ambindel: bool = True, insert3: bool = True, clip_end5: int = 0, clip_end3: int = 0, paired: bool = False)
- relate_truncated(num_fields: int, error_msg: str, ref: str = 'ref', refseq: DNA = DNA('ACGT'), read: DNA = DNA('ACGT'), qual: str = 'FFFF', cigar: str = '4M', end5: Any = 1, ambindel: bool = True, insert3: bool = True, clip_end5: int = 0, clip_end3: int = 0, paired: bool = False)
Test errors caused by lines that are too short.
- test_4nt_2ins()
- test_4nt_2ins_paired()
- test_5nt_2ins()
- test_6nt_2ins()
- test_7nt_0ins()
- test_8nt_0ins()
- test_all_matches()
- test_ambig_delet_low_qual()
Test ambiguous deletions with all low-quality positions.
- test_error_cigar_adj_ins_del()
- test_error_cigar_adj_int_del()
- test_error_cigar_consecutive()
- test_error_cigar_del_first_rel()
- test_error_cigar_del_last_rel()
- test_error_cigar_empty()
- test_error_cigar_ins_first_rel()
- test_error_cigar_ins_last_rel()
- test_error_cigar_int_first_rel()
- test_error_cigar_int_last_rel()
- test_error_cigar_missing()
- test_error_cigar_op_read_diff()
- test_error_cigar_op_ref_long()
- test_error_cigar_op_ref_zero()
- test_error_cigar_parse()
- test_error_cigar_soft_clips()
- test_error_flag_large()
- test_error_flag_missing()
- test_error_flag_parse()
- test_error_line_improper_flag_proper()
- test_error_line_paired_flag_unpaired()
- test_error_line_unpaired_flag_paired()
- test_error_mapq()
- test_error_mapq_insufficient()
- test_error_mapq_missing()
- test_error_name_missing()
- test_error_pos_large()
- test_error_pos_missing()
- test_error_pos_parse()
- test_error_pos_zero()
- test_error_qual_missing()
- test_error_read_missing()
- test_error_read_qual_diff()
- test_error_ref_mismatch()
- test_error_ref_missing()
- test_example_1()
Soft clips in CIGAR plus clip_end5 and clip_end3.
Seq GGTATAG Qul FFFFFFF CGR SS====S Ref CAATATATC Pos 123456789
- test_example_2()
Deletions cannot move out of soft-clipped regions.
Seq TATA–TAT Qul FFFF–FFF CGR SS==DD==S Ref ATATATATATA Pos 123456789ab
- test_example_3()
Introns cannot move out of soft-clipped regions.
Seq TATA__TAT Qul FFFF__FFF CGR SS==NN==S Ref ATATATATATA Pos 123456789ab
- test_example_4()
Insertions cannot move out of soft-clipped regions.
Seq TATATATAT Qul FFFFFFFFF CGR SS==II==S Ref ATATA–TATA Pos 12345–6789
- test_long_ambindels()
- test_n_read()
Read contains a non-ACGT base and reference is ACGT.
- test_n_ref()
Reference contains a non-ACGT base.
- test_soft_clips()
- class seismicrna.relate.tests.relate_test.TestMergeMates(methodName='runTest')
Bases:
TestCase- test_both_blank()
- test_both_reads()
- test_empty()
- test_overhangs()
- test_read1()
- test_read2()
- seismicrna.relate.tests.relate_test.as_sam(name: str, flag: int, ref: str, end5: int, mapq: int, cigar: str, rnext: str, pnext: int, tlen: int, read: DNA, qual: str, validate: bool = True)
Return a line in SAM format from the given fields.
- Parameters:
name (
str) – Name of the read.flag (
int) – SAM flag. Must be in [0, MAX_FLAG].ref (
str) – Name of the reference.end5 (
int) – Most 5’ position to which the read mapped (1-indexed).mapq (
int) – Mapping quality score.cigar (
str) – CIGAR string. Not checked for compatibility with the read.rnext (
str) – Name of the mate’s reference (if paired-end).pnext (
int) – Most 5’ position of the mate (if paired-end).tlen (
int) – Length of the template.read (
DNA) – Base calls in the read. Must be equal in length to read.qual (
str) – Phred quality score string of the base calls. Must be equal in length to read.validate (
bool) – Check that the fields are valid before assembling the line.
- Returns:
A line in SAM format containing the given fields.
- Return type:
- class seismicrna.relate.tests.sam_test.TestIterRecordsPaired(methodName='runTest')
Bases:
TestCase- test_blank()
- test_one_improper()
- test_one_proper()
- test_one_single()
- test_two_mated_improper()
- test_two_mated_improper_1()
- test_two_mated_improper_2()
- test_two_mated_proper()
- test_two_unmated_improper()
- test_two_unmated_proper()