Updated script to current sourmash api (4.8.3) #1
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ctb
reviewed
Oct 2, 2023
| @@ -12,13 +12,13 @@ def main(): | |||
| p.add_argument('-o', '--output', type=argparse.FileType('wt')) | |||
| args = p.parse_args() | |||
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| db = sourmash_lib.load_sbt_index(args.sbt) | |||
| db = sourmash.load_file_as_index(args.sbt) | |||
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| for n, leaf in enumerate(db.leaves()): | |||
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Suggested change
| for n, leaf in enumerate(db.leaves()): | |
| for n, leaf in enumerate(db.signatures()): |
this should make it work for any sourmash database, not just SBTs. But also for SBTs :)
Oh, and you'd need to change leaf.data.name to just leaf.name, since leaf would now be a SourmashSignature object.
Probably better to just rename leaf to ss or something.
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you could also grab db.manifest and iterate over rows; each element in rows is a dictionary containing row['name'] which will give you the info you want here, without actually loading the underlying sketch data.
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Tiny changes to the get-accessions-from-sbt.py file for building LCA tables. Now it works!