diff options
| -rw-r--r-- | gn3/computations/qtlreaper.py | 25 | ||||
| -rw-r--r-- | tests/unit/computations/test_qtlreaper.py | 105 |
2 files changed, 129 insertions, 1 deletions
diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py index 9b20309..8c0e6de 100644 --- a/gn3/computations/qtlreaper.py +++ b/gn3/computations/qtlreaper.py @@ -86,6 +86,31 @@ def run_reaper( subprocess.run(command_list, check=True) return (output_filename, permu_output_filename) +def organise_reaper_main_results(parsed_results): + def __organise_by_chromosome(chr_name, items): + chr_items = [item for item in items if item["Chr"] == chr_name] + return { + "Chr": str(chr_name), + "loci": [{ + "Locus": locus["Locus"], + "cM": locus["cM"], + "Mb": locus["Mb"], + "LRS": locus["LRS"], + "Additive": locus["Additive"], + "pValue": locus["pValue"] + } for locus in chr_items]} + + def __organise_by_id(identifier, items): + id_items = [item for item in items if item["ID"] == identifier] + unique_chromosomes = {item["Chr"] for item in id_items} + return { + "ID": identifier, + "chromosomes": [ + __organise_by_chromosome(chromo, id_items) + for chromo in sorted(unique_chromosomes)]} + + unique_ids = {res["ID"] for res in parsed_results} + return [__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 fd3434a..1d7347f 100644 --- a/tests/unit/computations/test_qtlreaper.py +++ b/tests/unit/computations/test_qtlreaper.py @@ -1,7 +1,9 @@ """Module contains tests for gn3.computations.qtlreaper""" from unittest import TestCase from gn3.computations.qtlreaper import ( - parse_reaper_main_results, parse_reaper_permutation_results) + parse_reaper_main_results, + organise_reaper_main_results, + parse_reaper_permutation_results) class TestQTLReaper(TestCase): """Class for testing qtlreaper interface functions.""" @@ -73,3 +75,104 @@ class TestQTLReaper(TestCase): 5.24619, 5.27961, 5.28228, 5.43903, 5.50188, 5.51694, 5.56830, 5.63874, 5.71346, 5.71936, 5.74275, 5.76764, 5.79815, 5.81671, 5.82775, 5.89659, 5.92117, 5.93396, 5.93396, 5.94957]) + + def test_organise_reaper_main_results(self): + self.assertEqual( + organise_reaper_main_results([ + { + "ID": "T1", "Locus": "rs31443144", "Chr": 1, "cM": 1.500, + "Mb": 3.010, "LRS": 0.500, "Additive": -0.074, + "pValue": 1.000 + }, + { + "ID": "T1", "Locus": "rs6269442", "Chr": 1, "cM": 1.500, + "Mb": 3.492, "LRS": 0.500, "Additive": -0.074, + "pValue": 1.000 + }, + { + "ID": "T1", "Locus": "rs32285189", "Chr": 1, "cM": 1.630, + "Mb": 3.511, "LRS": 0.500, "Additive": -0.074, + "pValue": 1.000 + }, + { + "ID": "T1", "Locus": "rs258367496", "Chr": 1, "cM": 1.630, + "Mb": 3.660, "LRS": 0.500, "Additive": -0.074, + "pValue": 1.000 + }, + { + "ID": "T1", "Locus": "rs32430919", "Chr": 1, "cM": 1.750, + "Mb": 3.777, "LRS": 0.500, "Additive": -0.074, + "pValue": 1.000 + }, + { + "ID": "T1", "Locus": "rs36251697", "Chr": 1, "cM": 1.880, + "Mb": 3.812, "LRS": 0.500, "Additive": -0.074, + "pValue": 1.000 + }, + { + "ID": "T1", "Locus": "rs30658298", "Chr": 1, "cM": 2.010, + "Mb": 4.431, "LRS": 0.500, "Additive": -0.074, + "pValue": 1.000 + }, + { + "ID": "T1", "Locus": "rs51852623", "Chr": 2, "cM": 2.010, + "Mb": 4.447, "LRS": 0.500, "Additive": -0.074, + "pValue": 1.000 + }, + { + "ID": "T1", "Locus": "rs31879829", "Chr": 2, "cM": 2.140, + "Mb": 4.519, "LRS": 0.500, "Additive": -0.074, + "pValue": 1.000 + }, + { + "ID": "T1", "Locus": "rs36742481", "Chr": 2, "cM": 2.140, + "Mb": 4.776, "LRS": 0.500, "Additive": -0.074, + "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 + }]}]}]) |