From 7805a48172ada364d3783db043dbcf637445a7fe Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 8 Oct 2021 22:07:43 +0000
Subject: Adding convert_dol_genotypes.py to scripts; everything is hard-coded
 in it since I was only writing it to generate a specific file and it probably
 won't be re-used

---
 scripts/convert_dol_genotypes.py | 68 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 68 insertions(+)
 create mode 100644 scripts/convert_dol_genotypes.py

diff --git a/scripts/convert_dol_genotypes.py b/scripts/convert_dol_genotypes.py
new file mode 100644
index 00000000..353f1b53
--- /dev/null
+++ b/scripts/convert_dol_genotypes.py
@@ -0,0 +1,68 @@
+# This is just to convert the Rqtl2 format genotype files for DOL into a .geno file
+# Everything is hard-coded since I doubt this will be re-used and I just wanted to generate the file quickly
+
+import os
+
+geno_dir = "/home/zas1024/gn2-zach/DO_genotypes/"
+markers_file = "/home/zas1024/gn2-zach/DO_genotypes/SNP_Map.txt"
+gn_geno_path = "/home/zas1024/gn2-zach/DO_genotypes/DOL.geno"
+
+marker_data = {}
+with open(markers_file, "r") as markers_fh:
+    for i, line in enumerate(markers_fh):
+        if i == 0:
+            continue
+        else:
+            line_items = line.split("\t")
+            this_marker = {}
+            this_marker['chr'] = line_items[2] if line_items[2] != "0" else "M"
+            this_marker['pos'] = f'{float(line_items[3])/1000000:.6f}'
+            marker_data[line_items[1]] = this_marker
+
+sample_names = []
+for filename in os.listdir(geno_dir):
+    if "gm4qtl2_geno" in filename:
+        with open(geno_dir + "/" + filename, "r") as rqtl_geno_fh:
+            for i, line in enumerate(rqtl_geno_fh):
+                line_items = line.split(",")
+                if i < 3:
+                    continue
+                elif not len(sample_names) and i == 3:
+                    sample_names = [item.replace("TLB", "TB") for item in line_items[1:]]
+                elif i > 3:
+                    marker_data[line_items[0]]['genotypes'] = ["X" if item.strip() == "-" else item.strip() for item in line_items[1:]]
+
+def sort_func(e):
+    try:
+        return int(e['chr'])
+    except:
+        if e['chr'] == "X":
+            return 20
+        elif e['chr'] == "Y":
+            return 21
+        elif e['chr'] == "M":
+            return 22
+
+marker_list = []
+for key, value in marker_data.items():
+    if 'genotypes' in value:
+        this_marker = {
+            'chr': value['chr'],
+            'locus': key,
+            'pos': value['pos'],
+            'genotypes': value['genotypes']
+        }
+        marker_list.append(this_marker)
+
+marker_list.sort(key=sort_func)
+
+with open(gn_geno_path, "w") as gn_geno_fh:
+    gn_geno_fh.write("\t".join((["Chr", "Locus", "cM", "Mb"] + sample_names)))
+    for marker in marker_list:
+        row_contents = [
+            marker['chr'],
+            marker['locus'],
+            marker['pos'],
+            marker['pos']
+        ] + marker['genotypes']
+        gn_geno_fh.write("\t".join(row_contents) + "\n")
-- 
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