sourmash sketch fromfile missing in v4.3?

[phiweger]

Maybe I am using this wrongly:

# https://sourmash.readthedocs.io/en/latest/sourmash-sketch.html#bulk-sketch-construction-from-many-files
sourmash sketch fromfile input.csv -p dna -o db.zip
#  sketch: error: argument subcmd: invalid choice: 'fromfile' (choose from 'dna', 'rna', 'nucleotide', 'nt', 'protein', 'aa', 'prot', 'translate')

[mr-eyes]

Hi,

Would you please post the whole command line output, including the version number?

[phiweger]

Thx for the quick reply. The above literally is the command line output, and sourmash --version is v4.3, fresh conda install.

[mr-eyes]

@phiweger Thank you! I am confirming the bug in version 4.3.0.

mamba create -n issue_2007 bioconda::sourmash
conda activate issue_2007
sourmash --version
# sourmash 4.3.0

sourmash sketch fromfile input.csv -p dna -o db.zip
# sketch: error: argument subcmd: invalid choice: 'fromfile' (choose from 'dna', 'rna', 'nucleotide', 'nt', 'protein', 'aa', 'prot', 'translate')

---

However, it's fixed in the current unreleased version, 4.3.1. In the meanwhile, you can install the latest version using the following command: pip install git+https://github.com/sourmash-bio/sourmash

You might need to install rust first conda install conda-forge::rust

Please let us know if you need further assistance.

[ctb]

hi, sketch fromfile is a new command and will be released in sourmash v4.4.0; see #1968 for our draft notes. Sorry 'bout that, normally we put in version markers for new commands. and forgot for this one!

I'll update the docs in a bit; please leave this issue open. Thanks!

[ctb]

see #2009.

[mr-eyes]

Resolving some confusion in my previous comments and also for future reference.

sourmash docs with readthedocs/latest is for the github/latest branch which may or may not reflect the latest sourmash release.

fromfile was a not-yet-implemented feature in sourmash <v4.4.0, and the latest released version is v4.3.0