Tessa Pierce Ward

- Check download wrapper - potentially remove `folder` option now that we don't need to independently download busco databases

see https://github.com/metagenome-atlas/clusterprofile/ especially: https://github.com/metagenome-atlas/clusterprofile/blob/master/%7B%7Bcookiecutter.profile_name%7D%7D/key_mapping.yaml

to do: - create `dammit report` option that runs `snakemake configfile --report`

database install fails with n_threads

1

see dib-lab/eelpond/issues/17 `dammit databases --install --database-dir /home/titus/eelpond/databases --busco-group metazoa --n_threads 4` ``` Installing... #### Run Tasks - [ ] download:Pfam-A.hmm.gz: * Cmd: `curl -o Pfam-A.hmm.gz ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam28.0/Pfam-A.hmm.gz` * Python: function check_hash...

would be nice to be able to do: ``` dammit databases --install --database-dir /database_dir \ --busco-group metazoa --busco-group eukaryota ``` Note that `annotate` works with this type of busco group...

useful python API functions

3

**1. A function that reads a sourmash signature file/database and raises exceptions if it runs into issues** ``` db = load_file_as_index(filename) ``` returns `None` if the file cannot be loaded....

[MRG] debias all containment values

5

Alternative to #2057. Instead of adding new functions to specifically use the debiased containment values, just debias within the original functions. This does alter the containment values slightly, but not...

Summarizing gather results with `sourmash taxonomy` is only valid across gather runs that used the same parameters. Now that `ksize`, `moltype` (and `scaled`?) are columns in the gather csv, we...

WIP: add manifest summarization

1

I went down a rabbithole while trying to write tests for safer selection... ended up implementing manifest summarization in rust. The output of `write_summary` mimics our current python manifest summarization...

move `signature::select` downsampling to `minhash()` or `get_sketch()`?

1

At the moment, we use `signature::select` to downsample minhashes if needed. However, this means we load the minhash during the `select`, which may happen during `sig_for_dataset`, for example, and then...