Add intensity to precursor table #687
Conversation
GeorgWa
requested review from
boopthesnoot,
mschwoer,
lucas-diedrich and
vbrennsteiner
| from alphadia.transferlearning.train import FinetuneManager | ||
| from alphadia.workflow.config import Config | ||
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| logger = logging.getLogger() |
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In which way is this change breaking? because it adds new columns to the output tables?
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| for config in quantlevel_configs: | ||
| lfq_df = lfq_results.get(config.level_name, pd.DataFrame()) |
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lfq_df = lfq_results.get(config.level_name)
if lfq_df is None:
continue
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| intensity_column = intensity_column_mapping.get( | ||
| config.level_name, f"{config.level_name}_intensity" |
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is the default required? you have e.g. "precursor": "precursor_intensity", explicitly defined
| from alphadia.outputtransform.search_plan_output import ( | ||
| LFQOutputConfig, | ||
| SearchPlanOutput, | ||
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| SearchPlanOutput, | ||
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| spo = SearchPlanOutput({"general": {"save_figures": False}}, "/tmp") |
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search_plan_output .. less mental mapping >> less characters
| SearchPlanOutput, | ||
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| spo = SearchPlanOutput({"general": {"save_figures": False}}, "/tmp") |
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/tmp => /some_output_path
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| result = spo._merge_quant_levels_to_psm(psm_df, lfq_results, configs) | ||
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| assert "precursor_intensity" in result.columns |
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this assert is redundant
| result = spo._merge_quant_levels_to_psm(psm_df, lfq_results, configs) | ||
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| assert "precursor_intensity" in result.columns | ||
| assert result["precursor_intensity"].iloc[0] == 100.0 |
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could be made stronger:
assert result["precursor_intensity"].values == [100.0]
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| def test_merge_quant_levels_to_psm_merges_protein_group_level(): | ||
| """Test that protein group level quantification is merged correctly.""" | ||
| from alphadia.outputtransform.search_plan_output import ( | ||
| LFQOutputConfig, | ||
| SearchPlanOutput, | ||
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| spo = SearchPlanOutput({"general": {"save_figures": False}}, "/tmp") | ||
| psm_df = pd.DataFrame({"pg": ["PG1"], "run": ["run1"]}) | ||
| lfq_results = {"pg": pd.DataFrame({"pg": ["PG1"], "run1": [700.0]})} | ||
| configs = [LFQOutputConfig("pg", "pg")] | ||
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| result = spo._merge_quant_levels_to_psm(psm_df, lfq_results, configs) | ||
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| assert "intensity" in result.columns | ||
| assert result["intensity"].iloc[0] == 700.0 |
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are these tests really adding something? if it works for one level, it should work for all..
I would rather add a test with multiple runs, or some edge cases
For a long time, precursor and peptide information was missing from the precursor output table.
This breaking change adds in the LFQ intensities for pprecursor, peptide and proteins