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Add misc/clinvar-vrsification #28

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Merged
theferrit32 merged 2 commits into from
Oct 8, 2025
Merged

Add misc/clinvar-vrsification #28

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b91689a
Add misc/clinvar-vrsification
theferrit32 Oct 8, 2025
b3dd64e
Fail on errors in misc/clinvar-vrsification
theferrit32 Oct 8, 2025
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26 changes: 26 additions & 0 deletions misc/clinvar-vrsification
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Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
#!/bin/bash

set -euo pipefail

if [ $# -lt 1 ]; then
echo "Usage: $0 RELEASE_DATE" >&2
exit 1
fi

release_date="$1"

bucket_root="clinvar-gks/${release_date}/dev"
gs_prefix="gs://${bucket_root}"
input_file="${gs_prefix}/vi.jsonl.gz"
log_file="${release_date}-noliftover.log"

uv run python clinvar_gk_pilot/main.py \
--filename "${input_file}" \
--parallelism 2 2>&1 \
| tee "${log_file}"

outfile="output/buckets/${bucket_root}/vi.jsonl.gz"
dest_path="${gs_prefix}/vi-normalized-no-liftover.jsonl.gz"

gcloud storage cp "${outfile}" "${dest_path}"
echo "Wrote to ${dest_path}"