BUG: sample_ids are strings for partitioning#398
Open
cherman2 wants to merge 2 commits into
Open
Conversation
cherman2
changed the title
ebolyen
reviewed
Jul 7, 2026
| manifest = pd.read_csv(mags.path / "MANIFEST", index_col=None) | ||
| manifest = manifest[manifest["sample-id"].isin(all_samples)] | ||
| manifest = \ | ||
| manifest[manifest["sample-id"].astype("string").isin(all_samples)] |
Member
There was a problem hiding this comment.
We might be able to coerce first (I think all of these columns are strings)
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Description
Enforces that sample id's are treated like strings when filtering manifests during partitioning.
a forum post found that if the id's are all numeric, this line filters them out and then they get a
rachis.core.exceptions.ValidationError: /tmp/qiime2/user/tmp/rachis-OutPath-ih9wwzbg/MANIFEST is not a(n) MultiMAGManifestFormat file: No sample records found in manifest, only observed comments, blank lines, and/or a header row.https://forum.qiime2.org/t/evaluate-bins-with-busco-in-moshpit-tutorial-4-1-6-section/34073/16
I am using this PR as a "Issue placeholder". This code change fixes the issues but I am open to alternative solutions
AI Disclosure
AI Usage Details