Purge

Sometimes a sequence type or allele ends up in your local database that really shouldn't be there. Maybe it's been flagged as contaminated, misassigned, or simply erroneous. Rather than wiping an entire scheme and re-downloading everything, mlstdb purge lets you surgically remove just the offending entry and rebuild the BLAST database in one go.

Basic Usage

# Remove an entire scheme
mlstdb purge --scheme salmonella

# Remove a single ST from a scheme
mlstdb purge --scheme salmonella --st 3

# Remove a specific allele (and all STs that reference it)
mlstdb purge --scheme salmonella --allele aroC:1

# Batch purge across multiple schemes from a YAML config
mlstdb purge --config purge_config.yaml

Options

Option	Short	Description	Default
`--scheme`	`-s`	Scheme name to purge (e.g. `salmonella`)	—
`--st`		ST number to remove	—
`--allele`	`-a`	Allele to remove, format `locus:number` (e.g. `aroC:3`)	—
`--config`	`-c`	Path to a YAML config file for batch purging	—
`--force`	`-f`	Skip confirmation prompts and force-delete shared alleles	Off
`--verbose`	`-v`	Show detailed output	Off
`--directory`	`-d`	Directory containing downloaded schemes	`pubmlst`
`--blast-directory`	`-b`	Directory for the BLAST database	`blast`
`-h`, `--help`		Show help

Note

Either --scheme or --config is required. You cannot mix --config with --scheme, --st, or --allele. Put those in the config file instead.

Purge modes

Purge an entire scheme

mlstdb purge --scheme salmonella

Deletes the entire pubmlst/salmonella/ directory (allele files, profile file, metadata, everything), and then rebuilds the BLAST database from the remaining schemes. You'll be asked to confirm before anything is deleted.

Use --force to skip the confirmation:

mlstdb purge --scheme salmonella --force

Purge a specific ST

mlstdb purge --scheme salmonella --st 3

Removes the row for ST 3 from salmonella.txt. For each allele in that row, mlstdb purge then checks whether the allele is referenced by any other ST:

Not used elsewhere → the allele entry is removed from the corresponding .tfa file (it's now an orphan. There's no point keeping it around)
Still used by other STs → a warning is printed and the allele is left untouched:

Allele aroC_1 is still used by ST 1, ST 2, ST 8 and 5 other STs — skipping.

If you want to force-delete shared alleles regardless, add --force:

mlstdb purge --scheme salmonella --st 3 --force

The BLAST database is rebuilt automatically at the end.

Purge a specific allele

mlstdb purge --scheme salmonella --allele aroC:1

Before removing anything, mlstdb purge checks which STs reference allele aroC_1 and reports them:

Allele aroC_1 is used by 6 STs: ST 1, ST 2, ST 8 and 3 others.
Remove allele aroC_1 and 6 affected ST(s)? [y/N]:

If you confirm (or use --force), it will:

Remove the aroC_1 entry from aroC.tfa
Remove all affected ST rows from salmonella.txt
Rebuild the BLAST database

This is the most thorough option. If a sequence itself is bad, it makes sense to clean out every ST built on it.

Purge an ST and check a specific allele

mlstdb purge --scheme salmonella --st 3 --allele aroC:1

A targeted combination: removes ST 3, then specifically checks whether allele aroC_1 has become an orphan as a result. If it has, it's removed too. If other STs still reference it, you'll see a warning (and --force overrides this as usual).

Batch purge with a config file

If you need to clean up multiple schemes in one go, use a YAML config file, the BLAST database is only rebuilt once at the end, which is much faster than running purge separately for each scheme.

Config format

# purge_config.yaml

purge:
  # Remove two alleles from salmonella
  - scheme: salmonella
    alleles:
      - aroC:1
      - dnaN:5

  # Remove two STs from klebsiella
  - scheme: klebsiella
    st:
      - 3
      - 15

  # Remove an ST and an allele from listeria_2
  - scheme: listeria_2
    st:
      - 42
    alleles:
      - abcZ:12

  # Remove the entire bordetella scheme
  - scheme: bordetella

# Optional global settings (can be overridden by CLI flags)
force: false
verbose: true
directory: pubmlst
blast_directory: blast

Then run:

mlstdb purge --config purge_config.yaml

CLI flags override the global settings in the config file. For example, to force all operations without being prompted:

mlstdb purge --config purge_config.yaml --force

Config keys

Key	Type	Description
`purge`	list	Required. List of scheme entries to process.
`scheme`	string	Required per entry. Must match a directory under `--directory`.
`st`	int or list of ints	ST number(s) to remove.
`alleles`	string or list of strings	Allele(s) to remove, in `locus:number` format.
`force`	bool	Skip confirmation prompts (default: `false`).
`verbose`	bool	Show detailed output (default: `false`).
`directory`	string	Schemes directory (default: `pubmlst`).
`blast_directory`	string	BLAST output directory (default: `blast`).

What gets rebuilt

After every purge operation, mlstdb purge automatically rebuilds the BLAST database from the remaining schemes in the data directory. This is the same process as mlstdb update. It concatenates all .tfa files across all scheme directories and runs makeblastdb.

Purging is permanent

Purged entries are deleted from disk and cannot be recovered. If you're unsure, take a backup of your pubmlst/ directory before running purge.

cp -r pubmlst/ pubmlst_backup/

To restore a purged scheme from scratch, just re-run mlstdb update. It will download it again.

Tips

Orphaned alleles are sequences no longer linked to any ST. mlstdb purge automatically removes them when you purge an ST (unless they're still in use elsewhere). This keeps your FASTA files tidy.
Using --force on allele removal will delete the allele even if other STs reference it, which may leave those STs with a missing allele entry. Only use --force if you're confident all the affected STs should go too or follow up with another purge to clean them up.
Custom directories: If your schemes aren't in the default pubmlst/ directory, use -d and -b to point purge to the right places:
```
mlstdb purge --scheme salmonella --st 3 -d my_schemes -b my_blast
```