diff options
Diffstat (limited to 'r_qtl/r_qtl2.py')
| -rw-r--r-- | r_qtl/r_qtl2.py | 27 |
1 files changed, 21 insertions, 6 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index 79a0656..bc3a86f 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -35,8 +35,16 @@ def control_data(zfile: ZipFile) -> dict: def with_non_transposed(zfile: ZipFile, member_key: str, cdata: dict, - func: Callable[[dict], dict] = lambda val: val) -> Iterator[dict]: - """Abstracts away common file-opening for non-transposed R/qtl2 files.""" + process_value: Callable[ + [dict], dict] = lambda val: val) -> Iterator[dict]: + """Process non-transposed file values + + Arguments: + zfile: A zipfile object from opening a R/qtl2 bundle. + member_key: A key to retrieve the member file to process from the file. + cdata: The control data from the R/qtl2 bundle read from the JSON/YAML file. + process_value: A function to process the values from the file. + """ def not_comment_line(line): return not line.startswith(cdata.get("comment.char", "#")) @@ -45,7 +53,7 @@ def with_non_transposed(zfile: ZipFile, filter(not_comment_line, io.TextIOWrapper(innerfile)), delimiter=cdata.get("sep", ",")) for row in reader: - yield func(row) + yield process_value(row) def __make_organise_by_id__(id_key): """Return a function to use with `reduce` to organise values by some @@ -66,10 +74,17 @@ def __batch_of_n__(iterable: Iterable, num): def with_transposed(zfile: ZipFile, member_key: str, cdata: dict, - merge_function: Callable[ + process_value: Callable[ [str, tuple[str, ...], tuple[str, ...]], tuple[dict, ...]]) -> Iterator[dict]: - """Abstracts away common file-opening for transposed R/qtl2 files.""" + """Process transposed file values + + Arguments: + zfile: A zipfile object from opening a R/qtl2 bundle. + member_key: A key to retrieve the member file to process from the file. + cdata: The control data from the R/qtl2 bundle read from the JSON/YAML file. + process_value: A function to process the values from the file. + """ with zfile.open(cdata[member_key]) as innerfile: lines = (tuple(field.strip() for field in line.strip().split(cdata.get("sep", ","))) @@ -84,7 +99,7 @@ def with_transposed(zfile: ZipFile, (row for batch in __batch_of_n__(lines, 300) for line in batch - for row in merge_function(id_key, headers, line)), + for row in process_value(id_key, headers, line)), {}).items(): yield row except StopIteration: |