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qiime2 / q2-vsearch

vsearch plugin for QIIME 2
BSD 3-Clause "New" or "Revised" License
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IMP: Remove sample ids from derep seqs sequences #74

Closed Oddant1 closed 3 years ago

Oddant1 commented 4 years ago

Closes #57, but we seem to have a problem.

Attempting to use the methods described in #57 (removing the --relabel-keep flag) didn't work. It caused the following.

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Adding strict=False causes the table to only have the sample_ids and the sequences to only have the sha

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So I took matters into my own hands and decided to manually strip the ids from the completed sequence output. Using the current method we get something that looks like this.

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This caused tests to explode because it looks like skbio wants those sample_ids in the sequences to be used as a description? I am hazy on what exactly is going on with skbio, but I suspect it's the reason we chose to use --relabel-keep in the first place, or part of the reason anyway.

thermokarst commented 3 years ago

Sorry to do this @Oddant1, but I'm going to close this PR (its not you, its me). I wrote up my thoughts on it, here: https://github.com/qiime2/q2-vsearch/issues/57#issuecomment-820755655. The TLDR is I don't think this is actually something that needs to be fixed, because I don't think q2-vsearch is broken. Thanks for putting this together, I appreciate it.