From 64ce38b45839b6305b009f6e28b0f852409e9bda Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Tue, 31 Aug 2021 10:45:11 +0300
Subject: 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.
---
 .../data/qtlreaper/main_output_sample.txt          | 11 +++++++++
 .../data/qtlreaper/permu_output_sample.txt         | 27 ++++++++++++++++++++++
 2 files changed, 38 insertions(+)
 create mode 100644 tests/unit/computations/data/qtlreaper/main_output_sample.txt
 create mode 100644 tests/unit/computations/data/qtlreaper/permu_output_sample.txt

(limited to 'tests/unit/computations/data')

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
-- 
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