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authorMuriithi Frederick Muriuki2021-08-31 10:45:11 +0300
committerMuriithi Frederick Muriuki2021-08-31 10:45:11 +0300
commit64ce38b45839b6305b009f6e28b0f852409e9bda (patch)
tree9b645ae004289b963704cd6503255f4f0c3ac06d /tests/unit/computations/data
parent750eff22f33fc8c78d529702369446e3acbdcae6 (diff)
downloadgenenetwork3-64ce38b45839b6305b009f6e28b0f852409e9bda.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.txt11
-rw-r--r--tests/unit/computations/data/qtlreaper/permu_output_sample.txt27
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