seismicrna.export package

Submodules

seismicrna.export.main.run(input_path: tuple[str, ...], *, samples_meta: str, refs_meta: str, all_pos: bool = True, force: bool = False, max_procs: int = 16, parallel: bool = True) → 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]

• max_procs (int) – Run up to this many processes simultaneously [keyword-only, default: 16]

• parallel (bool) – Run tasks in parallel or in series [keyword-only, default: True]

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: PosTable, order: 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_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_sect_metadata(top: Path, sample: str, ref: str, sect: str, all_pos: bool)

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

seismicrna.export.web.iter_clust_table_data(table: ClustFreqTable, order: int, clust: int)

seismicrna.export.web.iter_pos_table_data(table: PosTable, order: int, clust: int, all_pos: bool)

seismicrna.export.web.iter_pos_table_series(table: PosTable, order: int, clust: int, all_pos: bool)

seismicrna.export.web.iter_pos_table_struct(table: PosTable, order: int, clust: int)

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

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