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sourmash-bio / sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.
http://sourmash.readthedocs.io/en/latest/
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`lca index` could use some upgrading #1948

Open ctb opened 2 years ago

ctb commented 2 years ago

First, it doesn't pick up the k-mer size from the available signatures, so you have to specify it explicitly on the command line (unlike sourmash index, where you only need to specify -k if it's not obvious).

Second, when loading from a database it doesn't make use of manifests or progress loading stuff, so it will simply say "loading signatures ... 1 of 1".

So you get

... loading signature GCA_900761165.1 Clostridia bac (1 of 1)

instead of any kind of useful indication of how many are being loaded - ref https://github.com/sourmash-bio/sourmash/issues/1426, https://github.com/sourmash-bio/sourmash/issues/1877

ctb commented 2 years ago

actually, after watching sourmash index I think mostly what I want is the output like that:

...loading from 'gtdb-rs207.genomic-reps.dna.k31.zip' / 22340 sigs total

which is a progress indicator rather than a progress bar ;).

ctb commented 2 years ago

could be part of https://github.com/sourmash-bio/sourmash/issues/2198 refactoring.