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.
---
 gn3/computations/qtlreaper.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

(limited to 'gn3/computations')

diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py
index c058e14..3b8e4db 100644
--- a/gn3/computations/qtlreaper.py
+++ b/gn3/computations/qtlreaper.py
@@ -90,3 +90,21 @@ def run_reaper(
 
     subprocess.run(command_list, check=True)
     return (output_filename, permu_output_filename)
+
+
+def parse_reaper_main_results(results_file):
+    with open(results_file, "r") as infile:
+        lines = infile.readlines()
+
+    def __parse_line(line):
+        items = line.strip().split("\t")
+        return items[0:2] + [float(item) for item in items[2:]]
+
+    header = lines[0].strip().split("\t")
+    return [dict(zip(header, __parse_line(line))) for line in lines[1:]]
+
+def parse_reaper_permutation_results(results_file):
+    with open(results_file, "r") as infile:
+        lines = infile.readlines()
+
+    return [float(line.strip()) for line in lines]
-- 
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