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-rw-r--r--gn3/db/traits.py24
1 files changed, 24 insertions, 0 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index 1e29aff..1c6aaa7 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -743,3 +743,27 @@ def generate_traits_filename(base_path: str = TMPDIR):
"""Generate a unique filename for use with generated traits files."""
return "{}/traits_test_file_{}.txt".format(
os.path.abspath(base_path), random_string(10))
+
+def export_informative(trait_data: dict, inc_var: bool = False) -> tuple:
+ """
+ Export informative strain
+
+ This is a migration of the `exportInformative` function in
+ web/webqtl/base/webqtlTrait.py module in GeneNetwork1.
+
+ There is a chance that the original implementation has a bug, especially
+ dealing with the `inc_var` value. It the `inc_var` value is meant to control
+ the inclusion of the `variance` value, then the current implementation, and
+ that one in GN1 have a bug.
+ """
+ def __exporter__(acc, data_item):
+ if not inc_var or data_item["variance"] is not None:
+ return (
+ acc[0] + (data_item["sample_name"],),
+ acc[1] + (data_item["value"],),
+ acc[2] + (data_item["variance"],))
+ return acc
+ return reduce(
+ __exporter__,
+ filter(lambda td: td["value"] is not None, trait_data["data"].values()),
+ (tuple(), tuple(), tuple()))