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🐛 fix counts_fragments_features #143

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🐛 fix counts_fragments_features #143

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014be18
:bug: fix counts_fragments_features
mbuttner May 30, 2024
ee590b7
Merge branch 'main' into master
mbuttner Oct 31, 2024
45ac36c
Update tools.py
mbuttner Oct 31, 2024
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7 changes: 4 additions & 3 deletions muon/_atac/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -848,7 +848,7 @@ def count_fragments_features(
raise ValueError("No column with strand for features could be found")
strand_col = features.columns.values[np.where(f_cols == chrom_col)[0][0]]

fragments = pysam.TabixFile(adata.uns["files"]["fragments"], parser=pysam.asBed())
fragments = pysam.TabixFile(adata.uns["files"]["fragments"])
try:
# List of lists matrix is quick and convenient to fill by row
mx = lil_matrix((n_features, n), dtype=int)
Expand All @@ -867,7 +867,7 @@ def count_fragments_features(
f_from = f[start_col] - extend_upstream
f_to = f[end_col] + extend_downstream

for fr in fragments.fetch(f[chr_col], f_from, f_to):
for fr in fragments.fetch(f[chr_col], f_from, f_to, parser=pysam.asBed()):
try:
ind = adata.obs.index.get_loc(fr.name) # cell barcode (e.g. GTCAGTCAGTCAGTCA-1)
mx.rows[i].append(ind)
Expand All @@ -878,7 +878,8 @@ def count_fragments_features(
mx.data[i].append(1)
except:
pass

# The connection has to be closed
fragments.close()
# Faster to convert to csr first and then transpose
mx = mx.tocsr().transpose()

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