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caporaso-lab / mockrobiota

A public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.
http://mockrobiota.caporasolab.us
BSD 3-Clause "New" or "Revised" License
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adding auto-annotate and inventory compilation scripts, plus new annotation files #52

Closed nbokulich closed 7 years ago

nbokulich commented 7 years ago

@gregcaporaso would you mind reviewing?

Some big changes here — I generated two draft scripts, autoannotate-taxonomy.py and inventory-compiler.py, which automatically generate the expected-taxonomy.tsv files, database-identifiers.tsv, and inventory.tsv.

Then I did just that — all bacterial communities have new greengens and silva 97% and 99% OTU expected-taxonomy.tsv files and database-identifiers.tsv files. Others coming next.

This is a complete fix for #22 and #46 and a partial fix for #24

Probably need some clean up and inventory-compiler.py needs some work to automate whenever specific files are added (if it's possible — see notes).

nbokulich commented 7 years ago

Thanks @gregcaporaso ! I have pushed all requested changes (with the exception of code edits, as these are now moved to a new repo).

nbokulich commented 7 years ago

Thanks @gregcaporaso ! Have made that fix and pushed the changes.

gregcaporaso commented 7 years ago

Thanks @nbokulich, looks good!