io module

read_tsv

read_tsv(path: pathlib.Path, as_dict: Literal[False], **kwargs) → Generator[List[str], None, None]

read_tsv(path: pathlib.Path, as_dict: Literal[True], columns: List[str], **kwargs) → Generator[Dict[str, str], None, None]

Read a plain-text or gzip compressed TSV table.

When as_dict is False, return each row as a list using csv.reader().

When as_dict is True, return each row as a dict mapping from the column name to the corresponding value using csv.DictReader. columns will be used as the column names. If columns is omitted, the first row will be treated as the column names.

Additional arguments kwargs are passed to the underlying function.

Examples

>>> tsv_pth = Path('inheritance_gene_table.tsv.gz')
>>> reader = read_tsv(tsv_pth)
>>> header = next(reader); header
['gene', 'disease', 'modes_of_inheritance']
>>> row = next(reader); row[-1]
'autosomal recessive, autosomal dominant'

>>> reader = read_tsv(tsv_pth, as_dict=True)
>>> row_d = next(reader)
>>> row_d['gene']
'SDHA'

read_csv

read_csv(path, *, dialect='excel', as_dict=False, columns=None, **kwargs)

Read a plain-text or gzip compressed CSV table.

See read_tsv() for its usage.

read_lines

read_lines(path)

Read a plain-text or gzip compressed text per line.

Parameters

path (pathlib.Path) –

Return type

List[str]

Helpers

class unix_tab

Bases: csv.excel

The csv.Dialect to read TSV.

delimiter = '\t'

lineterminator = '\n'