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FastQC: fix UnicodeDecodeError parsing fastqc_data.txt (try latin-1 or fail gracefully) #2024

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merged 2 commits into from
Sep 3, 2023
Merged

FastQC: fix UnicodeDecodeError parsing fastqc_data.txt (try latin-1 or fail gracefully) #2024

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9496e66
Gracefully catch UnicodeDecodeError
vladsavelyev Sep 3, 2023
2083739
FastQC: fix `UnicodeDecodeError` parsing fastqc_data.txt (try latin-1…
vladsavelyev Sep 3, 2023
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14 changes: 12 additions & 2 deletions multiqc/modules/fastqc/fastqc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -64,8 +64,18 @@ def __init__(self):
# FastQC zip files should have just one directory inside, containing report
d_name = fqc_zip.namelist()[0]
try:
with fqc_zip.open(os.path.join(d_name, "fastqc_data.txt")) as fh:
r_data = fh.read().decode("utf8")
path = os.path.join(d_name, "fastqc_data.txt")
with fqc_zip.open(path) as fh:
r_data = fh.read()
try:
r_data = r_data.decode("utf8")
except UnicodeDecodeError as e:
log.debug(f"Could not parse {path} as Unicode: {e}, attempting the latin-1 encoding")
try:
r_data = r_data.decode("latin-1")
except Exception as e:
log.warning(f"Error reading FastQC data file {path}: {e}. Skipping sample {s_name}.")
continue
self.parse_fastqc_report(r_data, s_name, f)
except KeyError:
log.warning("Error - can't find fastqc_raw_data.txt in {}".format(f))
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