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Hotfix - explicitly read latin-1 encoding from fasta files #637

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Dec 31, 2023
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Hotfix - explicitly read latin-1 encoding from fasta files #637

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3 changes: 1 addition & 2 deletions workflow_flu_gisaid_ingest/scripts/chunk_sequences.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ def process_fasta_file(fasta_file, metadata, output_path, chunk_size=10_000):
# Get the date from the fasta file name, as a string
# file_date = Path(fasta_file).name.replace(".fa.gz", "")

with open(fasta_file, "rt") as fp:
with open(fasta_file, "rt", encoding="latin-1") as fp:
lines = fp.readlines()
for i, line in enumerate(lines):
# Strip whitespace
Expand Down Expand Up @@ -114,7 +114,6 @@ def process_fasta_file(fasta_file, metadata, output_path, chunk_size=10_000):
date_lookup = dict(zip(metadata.index, metadata["submission_date"]))

for name, seq in entries:

# Flush results if chunk is full
if chunk_i == chunk_size:
print("Writing {} sequences".format(chunk_i))
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