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Covariate, offset, and list readers¤

These readers normalize IID-like columns and prepare covariate, offset, and identifier files for sample alignment.

Read a tab-delimited sample table with a PLINK-style IID column.

The header must contain exactly one case-insensitive iid or #iid column. An optional fid or #fid column is dropped, and the IID column is normalized to iid. The strings NA, NULL, NaN, nan, and empty fields are read as missing values.

Arguments:

  • path_or_filename: Plain-text or gzip-compressed tab-delimited file.
  • keep_columns: Optional column names or zero-based indices to retain. The IID column is added automatically when omitted.
  • drop_columns: Optional column names or zero-based indices to remove. The IID column is retained even when requested for removal.

Returns:

A Polars frame with normalized iid and at least one data column.

Raises:

  • ValueError: If keep and drop selections are both supplied, the header is empty, exactly one IID-like column is not present, a requested column is missing, or no data columns remain.
  • TypeError: If a column selection mixes names and indices.

jaxqtl.io.read_offset_tsvlike(path_or_filename: str | os.PathLike, column: str | int | None = None) -> DataFrame ¤

Read a sample-aligned offset from a tab-delimited file.

Arguments:

  • path_or_filename: Plain-text or gzip-compressed table accepted by read_plink_style_tsvlike.
  • column: Name or zero-based index of the offset column. When omitted, the input must already contain exactly one non-IID column.

Returns:

A two-column Polars frame with columns iid and offset.

Raises:

  • ValueError: If column has an unsupported type or the selected table does not contain exactly one non-IID column.
  • TypeError: If column selection is invalid for read_plink_style_tsvlike.

jaxqtl.io.read_single_column_file(path_or_filename: str | os.PathLike) -> list ¤

Read stripped lines from a plain-text or gzip-compressed file.

A first line beginning with # is treated as a header and skipped. Later lines, including empty or comment-like lines, are returned after stripping whitespace.

Arguments:

  • path_or_filename: Input text file, optionally ending in .gz.

Returns:

A list of strings in file order.