Create human-readable taxonomy lookup table from precomputed database

[cvigilv]

I'm currently trying to use foldseek to prepare some datasets and I would like to check if the taxonomic information of Alphafold/Proteome matches the one I obtained from the FTP server of Alphafold.

Is there any way to convert the binary _taxonomy file into a tab-separated value?

Expected Behavior

Current Behavior

Steps to Reproduce (for bugs)

Please make sure to execute the reproduction steps with newly recreated and empty tmp folders.

Foldssek Output (for bugs)

Please make sure to also post the complete output of Spacepharer. You can use gist.github.com for large output.

Context

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Your Environment

Include as many relevant details about the environment you experienced the bug in.

• Git commit used (The string after "MMseqs Version:" when you execute foldseek without any parameters):
• Which foldseek version was used (Statically-compiled, self-compiled, Conda, etc.):
• For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation:
• Server specifications (especially CPU support for AVX2/SSE and amount of system memory):
• Operating system and version:

[milot-mirdita]

The easiest workaround for this is probably to use slightly abuse addtaxonomy:

mmseqs databases UniProtKB/Swiss-Prot sprot tmp
MMSEQS_FORCE_MERGE=1 mmseqs addtaxonomy sprot sprot_h out
tr -d '\000' out > sprot_headers_with_taxonomy.tsv

Adding a module that exports the nodes/names taxonomy dmp files, would also be possible, but that would need to come from an external contribution as I don't have time to implement this currently.

[milot-mirdita]

That also works the same way for foldseek, just use a Foldseek database and the foldseek binary instead of mmseqs.

[cvigilv]

Thanks! Will give it a test and come back if I encounter any problem