Cleanup Blastdb Volumes Py

cleanup-blastdb-volumes-py

Quick Start

• Command: cleanup-blastdb-volumes.py -db <dbname> -dbtype <prot|nucl> [-dry-run]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/cleanup-blastdb-volumes.py
• Full reference: See references/help.md

When To Use This Tool

• Remove orphaned BLAST database volumes after database updates or alias changes.
• Reclaim disk space when a .pal or .nal alias DB no longer references all volumes on disk.
• Audit what would be deleted first with -dry-run.
• Resolve clutter in BLAST DB directories found through BLASTDB or NCBI config lookup.

Common Patterns

# 1) Preview cleanup for a protein alias database
cleanup-blastdb-volumes.py \
  -db nr \
  -dbtype prot \
  -dry-run

# 2) Remove extra nucleotide volumes after review
cleanup-blastdb-volumes.py \
  -db nt \
  -dbtype nucl

# 3) Verbose preview when the DB is discovered via BLASTDB
BLASTDB=/data/blastdb \
cleanup-blastdb-volumes.py \
  -db swissprot \
  -dbtype prot \
  -dry-run \
  -verbose

Recommended Workflow

1. Confirm the target database is an alias-style BLAST DB with a .pal or .nal file.
2. Run -dry-run first and inspect the extra volumes listed from the alias file's DBLIST.
3. Re-run without -dry-run only after confirming the leftover volumes are genuinely stale.
4. Finish with blastdbcheck or a representative BLAST query if the database is business-critical.

Guardrails

• This script cleans alias databases; if there is no .pal or .nal file, it exits without doing useful work.
• Database lookup is path-sensitive: it searches the current directory, BLASTDB, and .ncbirc / ncbi.ini configuration.
• Always use -dry-run first because the non-dry mode deletes files immediately.
• The cleanup removes companion files for orphaned volumes, not just the .pin / .nin index stub.
• Both -db and -dbtype are required.