Example: search collection manifests directly

sourmash-bio/sourmash-examples#5

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This example follows from Example: use picklists and manifests to work with a small subset of a large database.

In #4, we see how to use a picklist to search a small subset of GTDB. But we can make this even simpler.

Build a manifest that you can search directly

Specifying the picklist is cumbersome if you want to search this database repeatedly. sourmash also lets you build a collection manifest that contains pointers into the database, using sig check (doc link).

To create the collection manifest, first make a "pathlist" file, a text file containing the paths of sourmash databases you want to work with. In this case, the file will only contain one pathname, the GTDB database.

ls gtdb-rs207.genomic-reps.dna.k31.zip > pathlist.txt

Then, run:

sourmash sig check --picklist shew-picklist.csv:name:name \
     pathlist.txt --save-manifest shew-mf.csv

which will create a manifest in shew-mf.csv for all the entries that match the given picklist.

You can now search this manifest file directly:

sourmash search shew-query.sig shew-mf.csv

Categories

This example belongs to the following categories:

• examples of using manifests
• advanced examples
• examples that need improvement