Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix(clump): read input files recursively #292

Merged
merged 2 commits into from
Dec 1, 2023
Merged

fix(clump): read input files recursively #292

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
893ceaa
fix(clump): read input files recursively
ireneisdoomed Dec 1, 2023
fc4b33e
Merge branch 'main' into il-clump-fix
d0choa Dec 1, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 6 additions & 2 deletions src/otg/clump.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,9 @@ def __post_init__(self: ClumpStep) -> None:
Raises:
ValueError: If study index and LD index paths are not provided for study locus.
"""
input_cols = self.session.spark.read.parquet(self.input_path).columns
input_cols = self.session.spark.read.parquet(
self.input_path, recursiveFileLookup=True
).columns
if "studyLocusId" in input_cols:
if self.study_index_path is None or self.ld_index_path is None:
raise ValueError(
Expand All @@ -59,7 +61,9 @@ def __post_init__(self: ClumpStep) -> None:
study_index=study_index, ld_index=ld_index
).clump()
else:
sumstats = SummaryStatistics.from_parquet(self.session, self.input_path)
sumstats = SummaryStatistics.from_parquet(
self.session, self.input_path, recursiveFileLookup=True
)
clumped_study_locus = sumstats.window_based_clumping(
locus_collect_distance=self.locus_collect_distance
)
Expand Down