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-rw-r--r--r_qtl/r_qtl2.py27
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: