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| author | zsloan | 2021-10-08 22:07:43 +0000 |
|---|---|---|
| committer | zsloan | 2021-10-08 22:07:43 +0000 |
| commit | 7805a48172ada364d3783db043dbcf637445a7fe (patch) | |
| tree | d5dfc28010597314b4fd71654742e28c7ce8f484 | |
| parent | 70f8ed53f85cfb42ca81ed6c3b4c9cf1060940e5 (diff) | |
| download | genenetwork2-7805a48172ada364d3783db043dbcf637445a7fe.tar.gz | |
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
| -rw-r--r-- | scripts/convert_dol_genotypes.py | 68 |
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")
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