seismicrna.export package

Submodules

seismicrna.export.main.run(input_path: Iterable[str | Path], *, samples_meta: str, refs_meta: str, all_pos: bool = True, force: bool = False, num_cpus: int = 4) → list[Path]

Export a file of each sample for the seismic-graph web app.

Parameters:

samples_meta (str) – Add sample metadata from this CSV file to exported results [keyword-only]
refs_meta (str) – Add reference metadata from this CSV file to exported results [keyword-only]
all_pos (bool) – Export all positions (not just unmasked positions) [keyword-only, default: True]
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.export.meta.combine_metadata(special_metadata: dict[str, Any], parsed_metadata: dict[Any, dict], item: Any, what: str = 'item')

seismicrna.export.meta.parse_refs_metadata(file: Path)

Parse a CSV file of metadata for each reference.

Parameters:: file (Path) – CSV file of metadata for each reference
Returns:: Parsed metadata for each reference
Return type:: dict

seismicrna.export.meta.parse_samples_metadata(file: Path)

Parse a CSV file of metadata for each sample.

Parameters:: file (Path) – CSV file of metadata for each sample
Returns:: Parsed metadata for each sample
Return type:: dict

seismicrna.export.web.conform_series(series: Series | DataFrame)

seismicrna.export.web.export_sample(top_sample: tuple[Path, str], *args, force: bool, **kwargs)

seismicrna.export.web.format_metadata(metadata: dict[str, Any]): Prefix each key with the metadata symbol.

seismicrna.export.web.get_db_structs(table: PositionTable, k: int | None = None, clust: int | None = None)

seismicrna.export.web.get_ref_metadata(top: Path, sample: str, ref: str, refs_metadata: dict[str, dict])

seismicrna.export.web.get_reg_metadata(top: Path, sample: str, ref: str, reg: str, all_pos: bool)

seismicrna.export.web.get_sample_data(top: Path, sample: str, tables: list[Table], *, samples_metadata: dict[str, dict], refs_metadata: dict[str, dict], all_pos: bool)

seismicrna.export.web.get_sample_metadata(sample: str, samples_metadata: dict[str, dict])

seismicrna.export.web.get_table_data(table: Table, all_pos: bool)

seismicrna.export.web.iter_clust_table_data(table: AbundanceTable, k: int, clust: int)

seismicrna.export.web.iter_pos_table_data(table: PositionTable, k: int, clust: int, all_pos: bool)

seismicrna.export.web.iter_pos_table_series(table: PositionTable, k: int, clust: int, all_pos: bool)

seismicrna.export.web.iter_pos_table_struct(table: PositionTable, k: int, clust: int)

seismicrna.export.web.iter_read_table_data(table: ReadTable, k: int, clust: int)

seismicrna.export.web.iter_table_data(table: Table, k: int, clust: int, all_pos: bool)