From 221c773daea839ecf0e50c196484bb91e3a6db33 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Wed, 1 Sep 2021 06:18:20 +0300
Subject: Implement parsing of genotype labels

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi

* gn3/db/genotypes.py: parse genotype labels
* tests/unit/db/test_genotypes.py: test that genotype labels are parsed
  correctly

  As part of parsing the genotype files into usable python data structures,
  this commit adds a function to parse the label lines (beginning with "@")
  into the appropriate values.
---
 gn3/db/genotypes.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

(limited to 'gn3/db')

diff --git a/gn3/db/genotypes.py b/gn3/db/genotypes.py
index 610ddde..2be3e1a 100644
--- a/gn3/db/genotypes.py
+++ b/gn3/db/genotypes.py
@@ -67,3 +67,23 @@ def __load_genotype_samples_from_plink(genotype_filename: str):
     """
     genofile = open(genotype_filename)
     return [line.split(" ")[1] for line in genofile]
+
+def parse_genotype_labels(lines: list):
+    """
+    Parse label lines into usable genotype values
+
+    DESCRIPTION:
+    Reworks
+    https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/utility/gen_geno_ob.py#L75-L93
+    """
+    acceptable_labels = ["name", "filler", "type", "mat", "pat", "het", "unk"]
+    def __parse_label(line):
+        label, value = [l.strip() for l in line[1:].split(":")]
+        if label not in acceptable_labels:
+            return None
+        if label == "name":
+            return ("group", value)
+        return (label, value)
+    return tuple(
+        item for item in (__parse_label(line) for line in lines)
+        if item is not None)
-- 
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