seismicrna.core.rna package

Subpackages

• seismicrna.core.rna.tests package
  • Submodules
    • TestFormatDbString
      • TestFormatDbString.test_deep_pairs()
      • TestFormatDbString.test_excess_pseudoknot()
      • TestFormatDbString.test_invalid_pair()
      • TestFormatDbString.test_invalid_pos3()
      • TestFormatDbString.test_invalid_pos5()
      • TestFormatDbString.test_multi_pseudoknot()
      • TestFormatDbString.test_no_pairs()
      • TestFormatDbString.test_one_pair()
      • TestFormatDbString.test_pseudoknot()
      • TestFormatDbString.test_repeat_pos3()
      • TestFormatDbString.test_repeat_pos5()
      • TestFormatDbString.test_shallow_pairs()
    • TestPairedMarks
      • TestPairedMarks.test_paired_marks()
    • TestParseDbString
      • TestParseDbString.test_dangling_closer()
      • TestParseDbString.test_dangling_opener()
      • TestParseDbString.test_deep_pairs()
      • TestParseDbString.test_multi_marks()
      • TestParseDbString.test_multi_pseudoknot()
      • TestParseDbString.test_no_pairs()
      • TestParseDbString.test_pseudoknot()
      • TestParseDbString.test_shallow_pairs()
    • TestConstants
      • TestConstants.test_unpaired()
    • TestDictToPairs
      • TestDictToPairs.test_empty()
      • TestDictToPairs.test_invalid_pair()
      • TestDictToPairs.test_invalid_position()
      • TestDictToPairs.test_missing_reverse_1()
      • TestDictToPairs.test_missing_reverse_2()
      • TestDictToPairs.test_normal()
    • TestDictToTable
      • TestDictToTable.test_empty()
      • TestDictToTable.test_normal()
    • TestFindEnclosingPairs
      • TestFindEnclosingPairs.test_nested()
      • TestFindEnclosingPairs.test_no_pairs()
      • TestFindEnclosingPairs.test_pseudoknotted()
    • TestPairsToDict
      • TestPairsToDict.test_conflicting_pair_1()
      • TestPairsToDict.test_conflicting_pair_2()
      • TestPairsToDict.test_empty()
      • TestPairsToDict.test_invalid_position()
      • TestPairsToDict.test_normal()
    • TestPairsToTable
      • TestPairsToTable.test_conflicting_pair_1()
      • TestPairsToTable.test_conflicting_pair_2()
      • TestPairsToTable.test_invalid_position_1()
      • TestPairsToTable.test_invalid_position_2()
      • TestPairsToTable.test_no_pairs()
      • TestPairsToTable.test_normal()
    • TestTableToDict
      • TestTableToDict.test_empty()
      • TestTableToDict.test_normal()
    • TestTableToPairs
      • TestTableToPairs.test_empty()
      • TestTableToPairs.test_normal()
    • TestComputeAucRoc
      • TestComputeAucRoc.test_all_false_positives()
      • TestComputeAucRoc.test_all_positions_unpaired()
      • TestComputeAucRoc.test_empty_prediction()
      • TestComputeAucRoc.test_empty_prediction_with_unpaired()
      • TestComputeAucRoc.test_invalid_dtype()
      • TestComputeAucRoc.test_invalid_dtype_for_unpaired()
      • TestComputeAucRoc.test_mixed_prediction()
      • TestComputeAucRoc.test_neither_paired_nor_unpaired()
      • TestComputeAucRoc.test_no_positions_unpaired()
      • TestComputeAucRoc.test_perfect_prediction()
    • TestComputeFprTpr
      • TestComputeFprTpr.test_all_false_positives()
      • TestComputeFprTpr.test_all_positions_unpaired()
      • TestComputeFprTpr.test_empty_prediction()
      • TestComputeFprTpr.test_empty_prediction_with_unpaired()
      • TestComputeFprTpr.test_invalid_dtype()
      • TestComputeFprTpr.test_invalid_dtype_for_unpaired()
      • TestComputeFprTpr.test_mixed_paired_unpaired()
      • TestComputeFprTpr.test_mixed_prediction()
      • TestComputeFprTpr.test_neither_paired_nor_unpaired()
      • TestComputeFprTpr.test_no_positions_unpaired()
      • TestComputeFprTpr.test_perfect_prediction()
    • TestComputeRocCurve
      • TestComputeRocCurve.test_all_false_positives()
      • TestComputeRocCurve.test_all_positions_unpaired()
      • TestComputeRocCurve.test_empty_prediction()
      • TestComputeRocCurve.test_empty_prediction_with_unpaired()
      • TestComputeRocCurve.test_invalid_dtype()
      • TestComputeRocCurve.test_invalid_dtype_for_unpaired()
      • TestComputeRocCurve.test_mixed_prediction()
      • TestComputeRocCurve.test_neither_paired_nor_unpaired()
      • TestComputeRocCurve.test_no_positions_unpaired()
      • TestComputeRocCurve.test_perfect_prediction()
    • TestCalcWfmi
      • TestCalcWfmi.test_all_unpaired()
      • TestCalcWfmi.test_all_vs_internal_pairs_1()
      • TestCalcWfmi.test_all_vs_internal_pairs_2()
      • TestCalcWfmi.test_completely_different_structures()
      • TestCalcWfmi.test_different_regions()
      • TestCalcWfmi.test_empty_region()
      • TestCalcWfmi.test_identical_structures()
      • TestCalcWfmi.test_internal_pairs_only()
      • TestCalcWfmi.test_mixed_paired_unpaired()
      • TestCalcWfmi.test_mixed_paired_unpaired_subset()
      • TestCalcWfmi.test_one_empty_one_paired()
      • TestCalcWfmi.test_pseudoknot_structures()
    • TestRNAStructure
      • TestRNAStructure.test_from_db_string()
      • TestRNAStructure.test_init_outside_region()
      • TestRNAStructure.test_init_success()
      • TestRNAStructure.test_is_paired()
      • TestRNAStructure.test_is_paired_internally()

Submodules

class seismicrna.core.rna.base.RNARegion(*, region: Region, **kwargs)

Bases: object

Region of an RNA sequence.

property end3

Position of the 3’ end of the region.

property end5

Position of the 5’ end of the region.

property init_args

Arguments needed to initialize a new instance.

property ref

Name of the reference sequence.

property reg

Name of the region.

renumber_from(seq5: int)

Return a new RNARegion renumbered starting from a position.

Parameters:

seq5 (int) – Position from which to start the new numbering system.

Returns:

RNARegion with renumbered positions.

Return type:

RNARegion

property seq

Sequence of the region as RNA.

property seq_record

subregion(end5: int, end3: int)

seismicrna.core.rna.convert.run_ct_to_db(input_path: Iterable[str | Path], *, force: bool = False, num_cpus: int = 4)

Convert connectivity table (CT) to dot-bracket (DB) files.

Parameters:

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

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

seismicrna.core.rna.convert.run_db_to_ct(input_path: Iterable[str | Path], *, force: bool = False, num_cpus: int = 4)

Convert dot-bracket (DB) to connectivity table (CT) files.

Parameters:

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

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

seismicrna.core.rna.ct.parse_ct_file(ct_path: str | Path)

Yield the title, region, and base pairs for each structure in a connectivity table (CT) file.

Parameters:

ct_path (str | Path) – Path of the CT file.

Return type:

Generator[tuple[str, Region, list[tuple[int, int]]], Any, None]

seismicrna.core.rna.db.format_db_string(pairs: Iterable[tuple[int, int]], length: int, seq5: int = 1)

Create a dot-bracket string from a list of base pairs.

seismicrna.core.rna.db.parse_db_file_as_pairs(db_path: str | Path, seq5: int = 1)

Yield the title, region, and base pairs for each structure in a dot-bracket (DB) file.

Parameters:

• db_path (str | Path) – Path of the DB file.

• seq5 (int = 1) – Number to give the 5’ position of the sequence.

Return type:

Generator[tuple[str, Region, list[tuple[int, int]]], Any, None]

seismicrna.core.rna.db.parse_db_file_as_strings(db_path: str | Path)

Return the sequence and dot-bracket strings from a dot-bracket file.

seismicrna.core.rna.db.parse_db_string(db_string: str, seq5: int = 1)

Parse a dot-bracket string into a list of base pairs.

seismicrna.core.rna.io.ct_to_db(ct_path: Path, db_path: Path | None = None, force: bool = False)

Write a dot-bracket (DB) file of structures in a connectivity table (CT) file.

seismicrna.core.rna.io.db_to_ct(db_path: Path, ct_path: Path | None = None, force: bool = False)

Write a connectivity table (CT) file of structures in a dot-bracket (DB) file.

seismicrna.core.rna.io.find_ct_region(ct_path: Path) → Region

Region shared among all structures in a CT file.

seismicrna.core.rna.io.from_ct(ct_path: str | Path, branch: str = '')

Yield an instance of an RNAStructure for each structure in a connectivity table (CT) file.

Parameters:

• ct_path (Path) – Path of the CT file.

• branch (str) – Branch of the workflow for folding (optional).

Returns:

RNA secondary structures from the CT file.

Return type:

Generator[RNAStructure, Any, None]

seismicrna.core.rna.io.from_db(db_path: str | Path, branch: str = '', seq5: int = 1)

Yield an instance of an RNAStructure for each structure in a dot-bracket (DB) file.

Parameters:

• db_path (Path) – Path of the DB file.

• branch (str) – Branch of the workflow for folding (optional).

• seq5 (int = 1) – Number to give the 5’ position of the sequence.

Returns:

RNA secondary structures from the CT file.

Return type:

Generator[RNAStructure, Any, None]

seismicrna.core.rna.io.renumber_ct(ct_in: Path, ct_out: Path, seq5: int, force: bool = False)

Renumber the last column of a connectivity table (CT) file.

Parameters:

• ct_in (Path) – Path of the input CT file.

• ct_out (Path) – Path of the output CT file.

• seq5 (int) – Number to give the 5’ position in the renumbered CT file.

• force (bool = False) – Overwrite the output CT file if it already exists.

seismicrna.core.rna.io.to_ct(structures: Iterable[RNAStructure], ct_path: Path, force: bool = False)

Write a connectivity table (CT) file of RNA structures.

Parameters:

• structures (Iterable[RNAStructure]) – RNA structures to write to the CT file.

• ct_path (Path) – Path of the CT file.

• force (bool = False) – Overwrite the output CT file if it already exists.

seismicrna.core.rna.io.to_db(structures: Iterable[RNAStructure], db_path: Path, force: bool = False)

Write a dot-bracket (DB) file of RNA structures.

Parameters:

• structures (Iterable[RNAStructure]) – RNA structures to write to the CT file.

• db_path (Path) – Path of the DB file.

• force (bool = False) – Overwrite the output DB file if it already exists.

seismicrna.core.rna.pair.dict_to_pairs(pair_dict: dict[int, int])

Tuples of the 5’ and 3’ position in each pair.

seismicrna.core.rna.pair.dict_to_table(pair_dict: dict[int, int], region: Region)

Series of every position in the region and the base to which it pairs, or 0 if it does not pair.

seismicrna.core.rna.pair.find_enclosing_pairs(table: Series)

Find the base pair that encloses each position.

seismicrna.core.rna.pair.find_root_pairs(pairs: Iterable[tuple[int, int]])

Return all pairs that are not contained by any other pair.

seismicrna.core.rna.pair.map_nested(pairs: Iterable[tuple[int, int]])

Map each pair to the pair in which it is nested.

seismicrna.core.rna.pair.pairs_to_dict(pairs: Iterable[tuple[int, int]])

Return a dictionary that maps each position to the base to which it pairs and contains no key for unpaired positions.

seismicrna.core.rna.pair.pairs_to_table(pairs: Iterable[tuple[int, int]], region: Region)

Series of every position in the region and the base to which it pairs, or 0 if it does not pair.

seismicrna.core.rna.pair.renumber_pairs(pairs: Iterable[tuple[int, int]], offset: int)

Renumber pairs by offsetting each number.

Parameters:

• pairs (Iterable[tuple[int, int]]) – Pairs to renumber.

• offset (int) – Offset by which to chage the numbering.

Returns:

Renumbered pairs, in the same order as given.

Return type:

Generator[tuple[int, int], Any, None]

seismicrna.core.rna.pair.table_to_dict(table: Series)

Dictionary of the 5’ and 3’ position in each pair.

seismicrna.core.rna.pair.table_to_pairs(table: Series)

Tuples of the 5’ and 3’ position in each pair.

class seismicrna.core.rna.profile.RNAProfile(*, sample: str, branches: dict[str, str], mus_reg: str, mus_name: str, mus: Series, **kwargs)

Bases: RNARegion

Mutational profile of an RNA.

property init_args

Arguments needed to initialize a new instance.

property profile

Name of the mutational profile.

seismicrna.core.rna.roc.compute_auc(fpr: ndarray, tpr: ndarray)

Compute the area under the curve (AUC) of the receiver operating characteristic (ROC).

Parameters:

• fpr (numpy.ndarray) – False positive rate (FPR) of the ROC curve.

• tpr (numpy.ndarray) – True positive rate (TPR) of the ROC curve.

Returns:

AUC-ROC

Return type:

float

seismicrna.core.rna.roc.compute_auc_roc(profile: Series, is_paired: Series, is_unpaired: Series | None = None)

Compute the receiver operating characteristic (ROC) and the area under the curve (AUC) to indicate how well mutation data agree with a structure.

Parameters:

• profile (pandas.Series) – Mutational profile with one index per position, where each value is the mutation rate at the position.

• is_paired (pandas.Series) – Boolean series with one index per position, where each value is True if the base at the position is paired, otherwise False.

• is_unpaired (pandas.Series | None) – Boolean series with one index per position, where each value is True if the base at the position is unpaired, otherwise False.

Returns:

AUC-ROC

Return type:

float

seismicrna.core.rna.roc.compute_roc_curve(profile: Series, is_paired: Series, is_unpaired: Series | None = None)

Compute the receiver operating characteristic (ROC) curve to indicate how well mutation data agree with a structure.

Parameters:

• profile (pandas.Series) – Mutational profile with one index per position, where each value is the mutation rate at the position.

• is_paired (pandas.Series) – Boolean series with one index per position, where each value is True if the base at the position is paired, otherwise False.

• is_unpaired (pandas.Series | None) – Boolean series with one index per position, where each value is True if the base at the position is unpaired, otherwise False.

Returns:

FPR and TPR axes, respectively, of the ROC curve.

Return type:

tuple[numpy.ndarray, numpy.ndarray]

seismicrna.core.rna.roc.compute_rolling_auc(profile: Series, *structs: Series, size: int, min_data: int = 2)

Compute the area under the curve (AUC) of the receiver operating characteristic (ROC) at each position using a sliding window.

Parameters:

• profile (pandas.Series) – Mutational profile with one index per position, where each value is the mutation rate at the position.

• *structs (pandas.Series) – Boolean series with one index per position; each element is the pairing status of a base at that position. Ignore values that are None.

• size (int) – Size of the window.

• min_data (int = 2) – Minimum number of data in a window to use it, otherwise NaN.

Returns:

AUC-ROC at each position.

Return type:

pandas.Series

class seismicrna.core.rna.state.RNAState(*, title: str, pairs: Iterable[tuple[int, int]], branch: str = '', **kwargs)

Bases: RNAStructure, RNAProfile

RNA secondary structure with mutation rates.

calc_auc(terminal_pairs: bool = True)

Calculate the area under the ROC curve (AUC-ROC).

Parameters:

terminal_pairs (bool) – Whether to count terminal base pairs as paired (if True) or as neither paired nor unpaired (if False).

calc_auc_rolling(size: int, min_data: int = 2, terminal_pairs: bool = True)

Calculate the area under the ROC curve (AUC-ROC).

Parameters:

• size (int) – Size of the window.

• min_data (int) – Minimum number of data in a window to use it, otherwise NaN.

• terminal_pairs (bool) – Whether to count terminal base pairs as paired (if True) or as neither paired nor unpaired (if False).

calc_roc(terminal_pairs: bool = True)

Calculate the receiver operating characteristic (ROC) curve.

Parameters:

terminal_pairs (bool) – Whether to count terminal base pairs as paired (if True) or as neither paired nor unpaired (if False).

classmethod from_struct_profile(struct: RNAStructure, profile: RNAProfile)

Make an RNAState from an RNAStructure and an RNAProfile.

class seismicrna.core.rna.struct.RNAStructure(*, title: str, pairs: Iterable[tuple[int, int]], branch: str = '', **kwargs)

Bases: RNARegion

Secondary structure of an RNA.

property ct_data

Convert the connectivity table to a DataFrame.

property ct_text

Connectivity table as text.

property ct_title

Header line for the CT file.

property db_string

Dot-bracket string (structure only).

property db_title

Header line for the DB file.

property dict

Map from each paired base to its partner.

classmethod from_db_string(db_string: str, seq: DNA | RNA | str, *, seq5: int = 1, ref: str, reg: str, **kwargs)

Create an RNAStructure from a dot-bracket string.

get_db_text(sequence: bool)

Dot-bracket record.

property init_args

Arguments needed to initialize a new instance.

property is_paired

Whether each base is paired.

property is_paired_internally

Whether each base is paired and between two other base pairs (no bulges or other unpaired bases next to it).

property is_paired_terminally

Whether each base is paired and terminates a consecutive stretch of base pairs (i.e. is not internally paired).

property is_unpaired

Whether each base is unpaired.

iter_root_modules()

property pairs

Base pairs in the structure.

property roots

All pairs that are not contained by any other pair.

class seismicrna.core.rna.struct.Rna2dPart(*regions: RNARegion, **kwargs)

Bases: object

Part of an RNA secondary structure.

class seismicrna.core.rna.struct.Rna2dStem(side1: RNARegion, side2: RNARegion, **kwargs)

Bases: Rna2dPart

An RNA stem (contiguous double helix).

property region3

property region5

class seismicrna.core.rna.struct.Rna2dStemLoop(region: RNARegion, **kwargs)

Bases: RnaJunction

An RNA loop at the end of a stem.

property region

class seismicrna.core.rna.struct.RnaJunction(*regions: RNARegion, **kwargs)

Bases: Rna2dPart

A junction between stems in an RNA structure.

seismicrna.core.rna.struct.calc_wfmi(struct1: RNAStructure, struct2: RNAStructure, terminal_pairs: bool = True)

Weighted Fowlkes-Mallows index between two structures.