From 3723cc8fe3977f292e636e98278b73c88b2b9677 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 20 Dec 2023 15:57:38 +0300
Subject: Read genotype files

---
 r_qtl/r_qtl2.py | 40 +++++++++++++++++++++++++++++++++++++++-
 1 file changed, 39 insertions(+), 1 deletion(-)

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index 9c9d67b..508d3eb 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -1,13 +1,20 @@
 """The R/qtl2 parsing and processing code."""
+import io
+import csv
 import json
 import yaml
 from pathlib import Path
-from typing import List, Union
+from functools import reduce
+from typing import Any, List, Union, Iterator
 from zipfile import ZipFile, ZipInfo, is_zipfile
 
 from quality_control.debug import __pk__
 from r_qtl.errors import InvalidFormat
 
+def thread_op(value, *functions):
+    """Thread the `value` through the sequence of `functions`."""
+    return reduce(lambda result, func: func(result), functions, value)
+
 def control_data(zfile: ZipFile) -> dict:
     """Retrieve the control file from the zip file info."""
     files = tuple(filename
@@ -24,6 +31,37 @@ def control_data(zfile: ZipFile) -> dict:
             if files[0].endswith(".json")
             else yaml.safe_load(zfile.read(files[0])))
 
+def genotype_metadata(zfile: ZipFile, cdata: dict) -> dict:
+    """Read Individual ID key and the marker names."""
+    # TODO: Handle transposed files
+    line_num = 0
+    with zfile.open(cdata["geno"]) as genofile:
+        for line in filter(lambda line: not line.startswith("#"),
+                           io.TextIOWrapper(genofile)):
+            line_parts = line.strip().split(cdata.get("sep", ","))
+            return {
+                "individual_id_key": line_parts[0].strip(),
+                "markers": tuple(marker.strip() for marker in line_parts[1:])
+            }
+
+def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
+    """Load the genotype file, making use of the control data."""
+    # TODO: Handle transposed files
+    with zfile.open(cdata["geno"]) as genofile:
+        reader = csv.DictReader(filter(lambda line: not line.startswith("#"),
+                                       io.TextIOWrapper(genofile)),
+                                delimiter=cdata.get("sep", ","))
+        for row in reader:
+            yield {
+                key: thread_op(
+                    value,
+                    # replace genotype codes
+                    lambda val: cdata["genotypes"].get(val, val),
+                    # replace N/A strings
+                    lambda val: (None if val in cdata["na.strings"] else val))
+                for key,value
+                in row.items()
+            }
 
 def read_r_qtl2_files(filepath: Path):
     """Read R/qtl2 format zip files."""
-- 
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