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authorFrederick Muriuki Muriithi2024-10-17 12:42:34 -0500
committerFrederick Muriuki Muriithi2024-10-17 12:43:50 -0500
commitcd0d415e691f46941fc3bd4a132ed3bdacd97931 (patch)
tree38b94d8c8c0f3509661c19020c7952b0eb6741b7 /scripts/rqtl2
parentfa7204e1e80e2ee94db54df85fb57d0c477fd7be (diff)
downloadgn-uploader-cd0d415e691f46941fc3bd4a132ed3bdacd97931.tar.gz
Extract common functions.
Diffstat (limited to 'scripts/rqtl2')
-rw-r--r--scripts/rqtl2/bundleutils.py44
1 files changed, 44 insertions, 0 deletions
diff --git a/scripts/rqtl2/bundleutils.py b/scripts/rqtl2/bundleutils.py
new file mode 100644
index 0000000..17faa7c
--- /dev/null
+++ b/scripts/rqtl2/bundleutils.py
@@ -0,0 +1,44 @@
+"""Common utilities to operate in R/qtl2 bundles."""
+from typing import Union, Callable
+
+def build_line_splitter(cdata: dict) -> Callable[[str], tuple[Union[str, None], ...]]:
+ """Build and return a function to use to split data in the files.
+
+ Parameters
+ ----------
+ cdata: A dict holding the control information included with the R/qtl2
+ bundle.
+
+ Returns
+ -------
+ A function that takes a string and return a tuple of strings.
+ """
+ separator = cdata["sep"]
+ na_strings = cdata["na.strings"]
+ def __splitter__(line: str) -> tuple[Union[str, None], ...]:
+ return tuple(
+ item if item not in na_strings else None
+ for item in
+ (field.strip() for field in line.strip().split(separator)))
+ return __splitter__
+
+
+def build_line_joiner(cdata: dict) -> Callable[[tuple[Union[str, None], ...]], str]:
+ """Build and return a function to use to split data in the files.
+
+ Parameters
+ ----------
+ cdata: A dict holding the control information included with the R/qtl2
+ bundle.
+
+ Returns
+ -------
+ A function that takes a string and return a tuple of strings.
+ """
+ separator = cdata["sep"]
+ na_strings = cdata["na.strings"]
+ def __joiner__(row: tuple[Union[str, None], ...]) -> str:
+ return separator.join(
+ (na_strings[0] if item is None else item)
+ for item in row)
+ return __joiner__