Add cached cd hit est reference collapse step to pathoscope#188
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- run cd-hit-est per segment with bounded concurrency - keep each cd-hit-est process single-threaded so proc controls segment-level parallelism
- allow isolates to omit schema segments during reference collapse - permit empty segment sentinels for unsegmented OTUs
igboyes
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Jun 29, 2026
igboyes
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igboyes
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utils.py is turning into a pig and should be modularized.
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| return { | ||
| "isolate_count_before": before_count, | ||
| "isolate_count_after": after_count, | ||
| "isolate_count_removed": before_count - after_count, | ||
| } |
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| def get_reference_index_path(work_path: Path) -> Path: | ||
| return work_path / "reference_index" / "reference" | ||
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| def get_collapsed_reference_path(work_path: Path) -> Path: | ||
| return work_path / "collapsed_reference" / "reference.json" | ||
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| def get_subtraction_indexes_path(work_path: Path) -> Path: | ||
| return work_path / "subtraction_indexes" | ||
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| def get_isolate_path(work_path: Path) -> Path: | ||
| return work_path / "isolates" | ||
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| def get_isolate_fasta_path(isolate_path: Path) -> Path: | ||
| return isolate_path / "isolate_index.fa" | ||
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| def get_isolate_fastq_path(isolate_path: Path) -> Path: | ||
| return isolate_path / "isolate_mapped.fq" | ||
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| def get_isolate_index_path(isolate_path: Path) -> Path: | ||
| return isolate_path / "isolates" | ||
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| def get_isolate_bam_path(isolate_path: Path) -> Path: | ||
| return isolate_path / "to_isolates.bam" | ||
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| def get_subtracted_bam_path(work_path: Path) -> Path: | ||
| return work_path / "subtracted.bam" |
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Should be inlined if only used once. No need for separate function declaration.
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| with open(collapsed_reference_dir / "collapse-manifest.json", "w") as handle: | ||
| json.dump(stats, handle) |
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to_thread.
Not to sure what the point of stats and this file is. Seems like debugging that should be a test?
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| log.info("collapsing reference", outcome="miss", source=str(index.json_path)) | ||
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| stats = await collapse_reference_json( |
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Why is this called stats? Is it not a "collapse-manifest"?
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| log.info("reference collapse complete", **stats) | ||
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| created = await cache.put(key, collapsed_reference_dir, params=params) |
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Add reference collapsing step to pathoscope