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fix: ZeroDivisionError in _ccbr_counts2density.py when flanking TSS bins have zero reads #122
Description
Summary
atac_tss rule crashes with ZeroDivisionError when running on genomes (e.g. hs1_chrR) where some genes have zero read coverage in the outermost TSS flanking bins.
Discovered during the Biowulf test run for PR #120.
Error
Traceback (most recent call last):
File "_ccbr_counts2density.py", line 22, in <module>
density[n2bin[i]] = density[n2bin[i]] * 1.0 / flankavg
ZeroDivisionError: float division by zero
Rule: atac_tss
Script: workflow/scripts/_ccbr_counts2density.py (line 22)
Root cause
flanksum = 0
for i in range(1, 11): # first 10 bins: positions -1995 to -1905
flanksum += density[n2bin[i]]
for i in range(391, 401): # last 10 bins: positions +1905 to +1995
flanksum += density[n2bin[i]]
flankavg = flanksum * 1.0 / 20 # <-- crashes if flanksum == 0flankavg is the mean read depth across the 10 outermost bins on each side of the ±2 kb TSS window. If a gene (e.g. on chrR) has zero reads in all 20 flanking bins, flankavg = 0 and the normalization on line 22 raises ZeroDivisionError.
Proposed fix
Guard against zero before the normalization loop. If flankavg == 0, emit 0.0 for all density values and report TSS enrichment as 0.0 rather than crashing:
flankavg = flanksum * 1.0 / 20
if flankavg == 0:
for i in range(1, 401):
print("%d\t%.4f" % (n2bin[i], 0.0))
print("# TSS enrichment: 0.0000")
sys.exit(0)Related
- Genome added by issue feat: add hs1_chrR as a supported reference genome #117 / PR feat: add hs1_chrR (T2T-CHM13 + rDNA unit) as a supported genome #120
- Companion annotation-script bug tracked separately
⚡ Generated using AI ⚡
Activity
[-]fix: hs1_chrR support broken in annotation scripts and TSS enrichment calculation[/-][+]fix: ZeroDivisionError in _ccbr_counts2density.py when flanking TSS bins have zero reads[/+]fix: guard against ZeroDivisionError in _ccbr_counts2density.py when …
kopardev commentedon Aug 4, 2026
Fixed in commit 19dcbf5 on branch
issue_117(folded into PR #120).Change in
workflow/scripts/_ccbr_counts2density.py: added a zero-guard immediately after computingflankavg. If all 20 flanking bins carry zero reads, the script now emits0.0for every density value and prints# TSS enrichment: 0.0000, then exits cleanly. This is the correct biological interpretation — a gene with no detectable background flanking the TSS has effectively zero TSS enrichment score.⚡ Generated using AI ⚡