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| author | Muriithi Frederick Muriuki | 2021-08-31 10:45:11 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2021-08-31 10:45:11 +0300 |
| commit | 64ce38b45839b6305b009f6e28b0f852409e9bda (patch) | |
| tree | 9b645ae004289b963704cd6503255f4f0c3ac06d /tests/unit/computations/data | |
| parent | 750eff22f33fc8c78d529702369446e3acbdcae6 (diff) | |
| download | genenetwork3-64ce38b45839b6305b009f6e28b0f852409e9bda.tar.gz | |
Parse QTLReaper outputs
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/qtlreaper.py: pass output files
* tests/unit/computations/data/qtlreaper/main_output_sample.txt: sample test
data
* tests/unit/computations/data/qtlreaper/permu_output_sample.txt: sample test
data
* tests/unit/computations/test_qtlreaper.py: add tests
Add code to parse the QTLReaper output data files.
Diffstat (limited to 'tests/unit/computations/data')
| -rw-r--r-- | tests/unit/computations/data/qtlreaper/main_output_sample.txt | 11 | ||||
| -rw-r--r-- | tests/unit/computations/data/qtlreaper/permu_output_sample.txt | 27 |
2 files changed, 38 insertions, 0 deletions
diff --git a/tests/unit/computations/data/qtlreaper/main_output_sample.txt b/tests/unit/computations/data/qtlreaper/main_output_sample.txt new file mode 100644 index 0000000..12b11b4 --- /dev/null +++ b/tests/unit/computations/data/qtlreaper/main_output_sample.txt @@ -0,0 +1,11 @@ +ID Locus Chr cM Mb LRS Additive pValue +T1 rs31443144 1 1.500 3.010 0.500 -0.074 1.000 +T1 rs6269442 1 1.500 3.492 0.500 -0.074 1.000 +T1 rs32285189 1 1.630 3.511 0.500 -0.074 1.000 +T1 rs258367496 1 1.630 3.660 0.500 -0.074 1.000 +T1 rs32430919 1 1.750 3.777 0.500 -0.074 1.000 +T1 rs36251697 1 1.880 3.812 0.500 -0.074 1.000 +T1 rs30658298 1 2.010 4.431 0.500 -0.074 1.000 +T1 rs51852623 1 2.010 4.447 0.500 -0.074 1.000 +T1 rs31879829 1 2.140 4.519 0.500 -0.074 1.000 +T1 rs36742481 1 2.140 4.776 0.500 -0.074 1.000 diff --git a/tests/unit/computations/data/qtlreaper/permu_output_sample.txt b/tests/unit/computations/data/qtlreaper/permu_output_sample.txt new file mode 100644 index 0000000..64cff07 --- /dev/null +++ b/tests/unit/computations/data/qtlreaper/permu_output_sample.txt @@ -0,0 +1,27 @@ +4.44174 +5.03825 +5.08167 +5.18119 +5.18578 +5.24563 +5.24619 +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 |