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BUG: sample_ids are strings for partitioning - #398
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cherman2
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ebolyen
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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)] |
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We might be able to coerce first (I think all of these columns are strings)
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Hey @ebolyen, this is ready for review (if needed) or merging. I added another set of MAGs with numerical IDs in the test and applied type coercion, as you suggested - it did fix the issue. |
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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
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