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

1 files changed, 68 insertions, 0 deletions

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")