From 69474e758208ccabe1ae0c4b62403c043a4cd7eb Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 25 Dec 2023 11:20:11 +0300
Subject: Read genetic map files

---
 r_qtl/r_qtl2.py | 30 +++++++++++++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index 508d3eb..94fa842 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -8,7 +8,6 @@ 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):
@@ -63,6 +62,35 @@ def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
                 in row.items()
             }
 
+def genetic_map_data(zfile: ZipFile, cdata: dict) -> dict:
+    """Read gmap files to get the genome mapping data"""
+    if not cdata.get("geno_transposed", False):
+        with zfile.open(cdata["gmap"]) as gmapfile:
+            reader = csv.DictReader(
+                filter(lambda line: not line.startswith("#"),
+                       io.TextIOWrapper(gmapfile)),
+                delimiter=cdata.get("sep", ","))
+            return {
+                line["marker"]: {
+                    key: value for key,value in line.items() if key != "marker"
+                } for line in reader
+            }
+
+    with zfile.open(cdata["gmap"]) as gmapfile:
+        lines = [[field.strip() for field in
+                  line.strip().split(cdata.get("sep", ","))]
+                 for line in
+                 filter(lambda line: not line.startswith("#"),
+                        io.TextIOWrapper(gmapfile))]
+
+    headers = tuple(line[0] for line in lines)
+    return reduce(
+        lambda gmap, row: {
+            **gmap,
+            row[0]: dict(zip(headers[1:], row[1:]))},
+        zip(*(line[1:] for line in lines)),
+        {})
+
 def read_r_qtl2_files(filepath: Path):
     """Read R/qtl2 format zip files."""
     with ZipFile(filepath, "r") as zfile:
-- 
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