From 8ababbb1cfbdbf3c26d9599253c6d45670c49046 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 25 Dec 2023 11:33:13 +0300
Subject: Generalise to read both genetic and physical maps.

---
 r_qtl/r_qtl2.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'r_qtl')

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index 94fa842..26d6dd4 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -62,10 +62,12 @@ def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
                 in row.items()
             }
 
-def genetic_map_data(zfile: ZipFile, cdata: dict) -> dict:
+def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> dict:
     """Read gmap files to get the genome mapping data"""
+    assert map_type in ("genetic-map", "physical-map"), "Invalid map type"
+    map_key = {"genetic-map": "gmap", "physical-map": "pmap"}[map_type]
     if not cdata.get("geno_transposed", False):
-        with zfile.open(cdata["gmap"]) as gmapfile:
+        with zfile.open(cdata[map_key]) as gmapfile:
             reader = csv.DictReader(
                 filter(lambda line: not line.startswith("#"),
                        io.TextIOWrapper(gmapfile)),
-- 
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