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generate tabix in working directory if not present #56

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generate tabix in working directory if not present #56

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0ed8710
generate tabix in working directory if not present
theAeon Aug 30, 2024
498faea
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 30, 2024
25a509d
Merge branch 'master' into tabix-create
theAeon Mar 7, 2025
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10 changes: 9 additions & 1 deletion ALLCools/count_matrix/dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -164,7 +164,15 @@ def _count_single_region_set(allc_table, region_config, obs_dim, region_dim):

total_data = []
for sample, allc_path in allc_table.items():
with pysam.TabixFile(allc_path) as allc:
try:
allc = pysam.TabixFile(allc_path)
except OSError:
local_tabix = "./" + pathlib.Path(allc_path).name + ".tbi"
local_compressed = pysam.tabix_index(
filename=allc_path, index=local_tabix, seq_col=0, start_col=1, end_col=1
)
allc = pysam.TabixFile(filename=local_compressed, index=local_tabix)
with allc:
region_ids = []
sample_data = []
region_chunks = pd.read_csv(region_config["regions"], index_col=0, chunksize=1000)
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