seismicrna.importmm package

Subpackages

• seismicrna.importmm.tests package
  • Submodules
    • TestIterMMFile
      • TestIterMMFile.setUp()
      • TestIterMMFile.tearDown()
      • TestIterMMFile.test_ref1_id()
      • TestIterMMFile.test_ref1_read0_single_mutation()
      • TestIterMMFile.test_ref1_read0_start_end()
      • TestIterMMFile.test_ref1_read1_two_mutations()
      • TestIterMMFile.test_ref1_read2_no_mutations()
      • TestIterMMFile.test_ref1_read_count()
      • TestIterMMFile.test_ref1_sequence()
      • TestIterMMFile.test_ref2_id()
      • TestIterMMFile.test_ref2_read0_mutation()
      • TestIterMMFile.test_ref2_read1_no_mutations()
      • TestIterMMFile.test_ref2_read_count()
      • TestIterMMFile.test_ref2_sequence()
      • TestIterMMFile.test_yields_two_transcripts()
    • TestBuildMutCodes
      • TestBuildMutCodes.test_acgt_all_positions()
      • TestBuildMutCodes.test_insert3_false_uses_ins5()
      • TestBuildMutCodes.test_insert3_true_base_a()
      • TestBuildMutCodes.test_insert3_true_base_c()
      • TestBuildMutCodes.test_insert3_true_base_g()
      • TestBuildMutCodes.test_insert3_true_base_n()
      • TestBuildMutCodes.test_insert3_true_base_t()
    • TestImportMM
      • TestImportMM.setUp()
      • TestImportMM.tearDown()
      • TestImportMM.test_min_reads_skips_ref2()
      • TestImportMM.test_ref1_batch_exists()
      • TestImportMM.test_ref1_refseq_exists()
      • TestImportMM.test_ref1_report_exists()
      • TestImportMM.test_ref1_report_n_reads_rel()
      • TestImportMM.test_ref1_report_n_reads_xam()
      • TestImportMM.test_ref1_report_ref()
      • TestImportMM.test_ref1_report_sample()
      • TestImportMM.test_ref2_batch_exists()
      • TestImportMM.test_ref2_refseq_exists()
      • TestImportMM.test_ref2_report_exists()
      • TestImportMM.test_ref2_report_n_reads_rel()
      • TestImportMM.test_ref2_report_n_reads_xam()
      • TestImportMM.test_ref2_report_ref()
      • TestImportMM.test_ref2_report_sample()
      • TestImportMM.test_result_paths_are_distinct()
      • TestImportMM.test_returns_two_paths()
    • TestRFCountIntegration
      • TestRFCountIntegration.test_matches_relate()

Submodules

seismicrna.importmm.main.run(input_path: Iterable[str | Path] = Sentinel.UNSET, *, sample: str = 'sim-sample', out_dir: str | Path = './out', branch: str = '', min_reads: int = 1000, batch_size: int = 65536, insert3: bool = True, write_read_names: bool = False, relate_pos_table: bool = True, relate_read_table: bool = False, brotli_level: int = 10, num_cpus: int = 4, force: bool = False, tmp_pfx='./tmp', keep_tmp=False)

Import RNA Framework Mutation Map (MM) files as relate outputs.

Parameters:

• sample (str) – Give this name to the simulated sample [keyword-only, default: ‘sim-sample’]

• out_dir (str | pathlib._local.Path) – Write all output files to this directory [keyword-only, default: ‘./out’]

• branch (str) – Create a new branch of the workflow with this name [keyword-only, default: ‘’]

• min_reads (int) – Discard alignment maps with fewer than this many reads [keyword-only, default: 1000]

• batch_size (int) – Limit batches to at most this many reads [keyword-only, default: 65536]

• insert3 (bool) – Mark each insertion on the base to its 3’ (True) or 5’ (False) side [keyword-only, default: True]

• write_read_names (bool) – Write the name of each read in a second set of batches (necessary for the options –mask-read or –mask-read-file) [keyword-only, default: False]

• relate_pos_table (bool) – Tabulate relationships per position for relate data [keyword-only, default: True]

• relate_read_table (bool) – Tabulate relationships per read for relate data [keyword-only, default: False]

• brotli_level (int) – Compress pickle files with this level of Brotli (0 - 11) [keyword-only, default: 10]

• num_cpus (int) – Use up to this many CPUs simultaneously [keyword-only, default: 4]

• force (bool) – Force all tasks to run, overwriting any existing output files [keyword-only, default: False]

• tmp_pfx – Write all temporary files to a directory with this prefix [keyword-only, default: ‘./tmp’]

• keep_tmp – Keep temporary files after finishing [keyword-only, default: False]

seismicrna.importmm.mm.iter_mm_file(mm_path: Path) → Iterator[tuple[str, DNA, list[tuple[int, int, list[int]]]]]

Iterate over transcript blocks in an MM file.

Yields (ref_id, refseq, reads) for each transcript, where reads is a list of (start, end, mut_positions) tuples (all positions 0-based).

seismicrna.importmm.write.import_mm(mm_path: Path, *, sample: str, out_dir: Path, tmp_dir: Path, branch: str, min_reads: int, batch_size: int, insert3: bool, write_read_names: bool, relate_pos_table: bool, relate_read_table: bool, brotli_level: int, force: bool) → list[Path]

Convert all transcript blocks in one MM file into relate outputs.

Returns a list of output directories (one per reference that was successfully imported).