diff options
| -rw-r--r-- | r_qtl/r_qtl2.py | 24 |
1 files changed, 22 insertions, 2 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index 93b8c8e..8c17362 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -5,7 +5,7 @@ import json from pathlib import Path from zipfile import ZipFile from functools import reduce, partial -from typing import Iterator, Iterable, Callable, Optional +from typing import Union, Iterator, Iterable, Callable, Optional import yaml @@ -302,7 +302,7 @@ def raw_file_data(zipfilepath: Union[str, Path], zfile.open(memberfilename) as innerfile): wrappedfile = io.TextIOWrapper(innerfile) for line in wrappedfile: - yield line.strip() + yield line def strip_comments(rawdata: Iterator[str], commentchar) -> Iterator[str]: """Remove comments from raw text.""" @@ -334,3 +334,23 @@ def read_control_file(zipfilepath: Union[str, Path]) -> dict: if bool(cdata.get(ftype)) } } + + +def read_file_data( + zipfilepath: Union[str, Path], + memberfilename: str, + processfile: Callable[[Iterator[str]], Iterator[str]] = lambda itr: itr, + processline: Callable[[str], str] = lambda line: line, + processfield: Callable[ + [Optional[str]], Optional[str]] = lambda val: val) -> Iterator[ + tuple[Optional[str], ...]]: + """Read a single file from the bundle processing each field.""" + cdata = read_control_file(zipfilepath) + return ( + tuple(processfield(field.strip()) + for field in processline(row.strip()).split(cdata["sep"])) + for row in + processfile( + strip_comments( + raw_file_data(zipfilepath, memberfilename), + cdata["comment.char"]))) |