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feat(IPVC-2478): updates/fixes to UTA files found during testing #43

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merged 2 commits into from
Jul 10, 2024

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bsgiles73
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@bsgiles73 bsgiles73 commented Jul 8, 2024

During the final build and testing of the UTA data release several issues were found and fixed...

  1. Update methods that write out txinfo to add in the new codon_table column (misc/refseq-historical-backfill/ncbi_extract_gbff.py & sbin/ncbi-parse-gbff).
  2. Fix uic config to point at Invitae internal server
  3. Add misc/export_mappings.py to repo. Used to compare content from new version to the last.
  4. Remove schema version and set role command from misc/generate_alingment_metrics.py.
  5. Update data name in sbin/update_ncbi script.
  6. Add tx_def_summary_v to initial alembic script.
  7. Add hgnc to the tx_similarity_v view.
  8. Add tx_exon_aln_mv to the refresh_matviews command.

@bsgiles73 bsgiles73 requested review from sptaylor and nvta1209 July 8, 2024 23:54

def parse_args():
parser = argparse.ArgumentParser(
description="Generate alignment metrics for transcript alignments"
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Should the description be updated for this script?

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Yes, they should!

@bsgiles73 bsgiles73 merged commit 2af4ec5 into main Jul 10, 2024
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@bsgiles73 bsgiles73 deleted the IPVC-2478-updates-from-testing branch July 10, 2024 20:00
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2 participants