Skip to content

fix: resolve KeyError and fragile array slicing in haplotypes_frequencies_advanced()` #982

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

Open
blankirigaya wants to merge 3 commits into
base: master
Choose a base branch
from
Open

fix: resolve KeyError and fragile array slicing in haplotypes_frequencies_advanced()` #982

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
291bb13
added astype(bool)
blankirigaya Feb 28, 2026
0ca2ab2
fixed repeated variable issue
blankirigaya Feb 28, 2026
e5e5c42
Merge branch 'master' into fixed-haq_frq
jonbrenas May 27, 2026
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
11 changes: 7 additions & 4 deletions malariagen_data/anoph/hap_frq.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -271,19 +271,22 @@ def haplotypes_frequencies_advanced(
ds_out[f"cohort_{coh_col}"] = "cohorts", df_cohorts[coh_col]

# Label the haplotypes
ds_out["variant_label"] = "variants", df_haps_sorted["label"]
ds_out["variant_label"] = "variants", df_haps_sorted["label"].values
# Event variables.
freq_cols_name = [c for c in df_haps_sorted.columns if c.startswith("frq_")]
count_cols_name = [c for c in df_haps_sorted.columns if c.startswith("count_")]
nobs_cols_name = [c for c in df_haps_sorted.columns if c.startswith("nobs_")]
ds_out["event_frequency"] = (
("variants", "cohorts"),
df_haps_sorted.to_numpy()[:, : len(df_cohorts)],
df_haps_sorted[freq_cols_name].to_numpy(),
)
ds_out["event_count"] = (
("variants", "cohorts"),
df_haps_sorted.to_numpy()[:, len(df_cohorts) : 2 * len(df_cohorts)],
df_haps_sorted[count_cols_name].to_numpy(),
)
ds_out["event_nobs"] = (
("variants", "cohorts"),
df_haps_sorted.to_numpy()[:, 2 * len(df_cohorts) : -2],
df_haps_sorted[nobs_cols_name].to_numpy(),
)

# Add confidence intervals.
Expand Down
Loading