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| author | Muriithi Frederick Muriuki | 2021-09-08 10:56:56 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2021-09-08 10:56:56 +0300 |
| commit | a718069c757bea9f7ecbaee25e23bd581750f906 (patch) | |
| tree | 0d04f09fa39bee446968a494f3713281aa264476 | |
| parent | 3f323734fcf258d28f3f7d33fdc1518ef9ec24a8 (diff) | |
| download | genenetwork3-a718069c757bea9f7ecbaee25e23bd581750f906.tar.gz | |
Ease search for traits and chromosomes
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Return a dict of values rather than list for the traits and chromosomes to
ease searching through the data.
| -rw-r--r-- | gn3/computations/qtlreaper.py | 9 | ||||
| -rw-r--r-- | tests/unit/computations/test_qtlreaper.py | 92 |
2 files changed, 52 insertions, 49 deletions
diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py index 02d6572..5180853 100644 --- a/gn3/computations/qtlreaper.py +++ b/gn3/computations/qtlreaper.py @@ -110,12 +110,15 @@ def organise_reaper_main_results(parsed_results): unique_chromosomes = {item["Chr"] for item in id_items} return { "ID": identifier, - "chromosomes": [ + "chromosomes": {_chr["Chr"]: _chr for _chr in [ __organise_by_chromosome(chromo, id_items) - for chromo in sorted(unique_chromosomes)]} + for chromo in sorted( + unique_chromosomes, key=chromosome_sorter_key_fn)]}} unique_ids = {res["ID"] for res in parsed_results} - return [__organise_by_id(_id, parsed_results) for _id in sorted(unique_ids)] + return { + trait["ID"]: trait for trait in + [__organise_by_id(_id, parsed_results) for _id in sorted(unique_ids)]} def parse_reaper_main_results(results_file): """ diff --git a/tests/unit/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py index 1d7347f..495ed97 100644 --- a/tests/unit/computations/test_qtlreaper.py +++ b/tests/unit/computations/test_qtlreaper.py @@ -130,49 +130,49 @@ class TestQTLReaper(TestCase): "pValue": 1.000 } ]), - [{"ID": "T1", - "chromosomes": [ - {"Chr": "1", - "loci": [ - { - "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010, - "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 - }, - { - "Locus": "rs6269442", "cM": 1.500, "Mb": 3.492, - "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 - }, - { - "Locus": "rs32285189", "cM": 1.630, "Mb": 3.511, - "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 - }, - { - "Locus": "rs258367496", "cM": 1.630, "Mb": 3.660, - "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 - }, - { - "Locus": "rs32430919", "cM": 1.750, "Mb": 3.777, - "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 - }, - { - "Locus": "rs36251697", "cM": 1.880, "Mb": 3.812, - "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 - }, - { - "Locus": "rs30658298", "cM": 2.010, "Mb": 4.431, - "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 - }]}, - {"Chr": "2", - "loci": [ - { - "Locus": "rs51852623", "cM": 2.010, "Mb": 4.447, - "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 - }, - { - "Locus": "rs31879829", "cM": 2.140, "Mb": 4.519, - "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 - }, - { - "Locus": "rs36742481", "cM": 2.140, "Mb": 4.776, - "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 - }]}]}]) + {"T1": {"ID": "T1", + "chromosomes": { + 1: {"Chr": 1, + "loci": [ + { + "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010, + "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 + }, + { + "Locus": "rs6269442", "cM": 1.500, "Mb": 3.492, + "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 + }, + { + "Locus": "rs32285189", "cM": 1.630, "Mb": 3.511, + "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 + }, + { + "Locus": "rs258367496", "cM": 1.630, "Mb": 3.660, + "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 + }, + { + "Locus": "rs32430919", "cM": 1.750, "Mb": 3.777, + "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 + }, + { + "Locus": "rs36251697", "cM": 1.880, "Mb": 3.812, + "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 + }, + { + "Locus": "rs30658298", "cM": 2.010, "Mb": 4.431, + "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 + }]}, + 2: {"Chr": 2, + "loci": [ + { + "Locus": "rs51852623", "cM": 2.010, "Mb": 4.447, + "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 + }, + { + "Locus": "rs31879829", "cM": 2.140, "Mb": 4.519, + "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 + }, + { + "Locus": "rs36742481", "cM": 2.140, "Mb": 4.776, + "LRS": 0.500, "Additive": -0.074, "pValue": 1.000 + }]}}}}) |