From b37a9c6c495d142852d0cee54d83f5c9e815e37b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 8 Oct 2021 22:19:07 +0000
Subject: Fixed the sort to account for both chr and pos in a kind of hack-y
 way + added some comments + changed EOL to LF because the file suddenly
 started including EOL characters

---
 scripts/convert_dol_genotypes.py | 142 ++++++++++++++++++++-------------------
 1 file changed, 74 insertions(+), 68 deletions(-)

(limited to 'scripts')

diff --git a/scripts/convert_dol_genotypes.py b/scripts/convert_dol_genotypes.py
index 353f1b53..81b3bd6d 100644
--- a/scripts/convert_dol_genotypes.py
+++ b/scripts/convert_dol_genotypes.py
@@ -1,68 +1,74 @@
-# 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")
+# 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"
+
+# Iterate through the SNP_Map.txt file to get marker positions
+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
+
+# Iterate through R/qtl2 format genotype files and pull out the samplelist and genotypes for each 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:]]
+
+# Generate list of marker obs to iterate through when writing to .geno file
+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)
+
+def sort_func(e):
+    """For ensuring that X/Y chromosomes/mitochondria are sorted to the end correctly"""
+    try:
+        return float((e['chr']))*1000 + float(e['pos'])
+    except:
+        if e['chr'] == "X":
+            return 20000 + float(e['pos'])
+        elif e['chr'] == "Y":
+            return 21000 + float(e['pos'])
+        elif e['chr'] == "M":
+            return 22000 + float(e['pos'])
+
+# Sort markers by chromosome
+marker_list.sort(key=sort_func)
+
+# Write lines to .geno file
+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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