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

SNP scoring optimizations #22

Merged
merged 8 commits into from
Apr 9, 2024
Merged

SNP scoring optimizations #22

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
d99e8b8
dok is empirically faster
davek44 Apr 1, 2024
4e38acd
strand transform scores instead of predictions
davek44 Apr 1, 2024
c033a82
concurrent futures
davek44 Apr 4, 2024
528892e
delete old score code
davek44 Apr 4, 2024
0ca1681
black
davek44 Apr 4, 2024
6f0ee9b
add strand_transform to fix pytest error
lruizcalico Apr 9, 2024
0c8021b
add strand_transform to hound_ism_bed line 278 fix missing arg
lruizcalico Apr 9, 2024
95e0b09
put None for strand_transform in hound_ism_bed hound_ism_snp to pass …
lruizcalico Apr 9, 2024
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
3 changes: 1 addition & 2 deletions src/baskerville/dataset.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -319,7 +319,7 @@ def make_strand_transform(targets_df, targets_strand_df):
targets_strand_df (pd.DataFrame): Targets DataFrame, with strand pairs collapsed.

Returns:
scipy.sparse.csr_matrix: Sparse matrix to sum strand pairs.
scipy.sparse.dok_matrix: Sparse matrix to sum strand pairs.
"""

# initialize sparse matrix
Expand All @@ -336,7 +336,6 @@ def make_strand_transform(targets_df, targets_strand_df):
if target.identifier[-1] == "-":
sti += 1
ti += 1
strand_transform = strand_transform.tocsr()

return strand_transform

Expand Down
2 changes: 1 addition & 1 deletion src/baskerville/scripts/hound_ism_bed.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -276,7 +276,7 @@ def main():
alt_preds = np.array(alt_preds)

ism_scores = snps.compute_scores(
ref_preds, alt_preds, options.snp_stats
ref_preds, alt_preds, options.snp_stats, None
)
for snp_stat in options.snp_stats:
scores_h5[snp_stat][si, mi - mut_start, ni] = ism_scores[
Expand Down
3 changes: 2 additions & 1 deletion src/baskerville/scripts/hound_ism_snp.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -156,6 +156,7 @@ def main():
else:
targets_strand_df = targets_df
strand_transform = None

num_targets = targets_strand_df.shape[0]

#################################################################
Expand Down Expand Up @@ -249,7 +250,7 @@ def main():
alt_preds = np.array(alt_preds)

ism_scores = snps.compute_scores(
ref_preds, alt_preds, options.snp_stats
ref_preds, alt_preds, options.snp_stats, None
)
for snp_stat in options.snp_stats:
scores_h5[snp_stat][si, mi - mut_start, ni] = ism_scores[
Expand Down
Loading
Loading