Fix add_sample_from_csv crash on unmatched transcript/gene ids (2.0.7) - #44
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…e id The gene_id/chr column construction used a list comprehension inside try/except KeyError -- if even one transcript_id or gene_id from the coverage csv wasn't found in the transcripts file, the whole comprehension raised and the column silently never got created for *any* row, crashing later with a confusing AttributeError far from the real cause (e.g. 'Series' object has no attribute 'chr'). Switch to per-row .get() lookups with explicit filtering, so one unmatched id only drops that row. Also make the warning actionable: point at infer_genes=True when gene info can't be resolved, which is the actual fix for files with no gene lines (e.g. PacBio isoseq-collapse/Pigeon output). Closes #25.
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Summary
Closes #25:
add_sample_from_csvcrashed with a confusingAttributeErrorwhen importing PacBio isoseq-collapse/Pigeon-style files that have nogenelines.TypeErroroninfer_genesis already fixed on master (side effect of Trouble while working with .csi indexes #28's fix in 2.0.3).AttributeErrorwas deeper than it looked:gene_id/chrcolumn construction used a list comprehension insidetry/except KeyError-- one unmatched id silently broke the column for every row, not just that one, crashing far downstream with an unrelated-looking error.Fix: per-row
.get()lookups with explicit filtering, so an unmatched id only drops that row. The warning is now also actionable, pointing atinfer_genes=Truewhen gene info can't be resolved -- confirmed as the actual fix against the reporter's scenario.Bumps version to 2.0.7.
Test plan
pytestsuite passes (19 passed), including the new regression testflake8/blackcleanpython -m build+twine check dist/*pass at 2.0.7