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+#!/usr/bin/env python3
+"""A script that generates the genotype files for groups of individuals, using an existing strain genotype file as a basis
+
+Example commands:
+python3 gen_ind_genofiles.py
+ /home/zas1024/gn2-zach/genotype_files/genotype/
+ /home/zas1024/gn2-zach/new_geno/
+ BXD-Micturition.geno
+ BXD.json
+python3 gen_ind_genofiles.py
+ /home/zas1024/gn2-zach/genotype_files/genotype
+ /home/zas1024/gn2-zach/new_geno/
+ BXD-Micturition.geno
+ BXD.2.geno BXD.4.geno BXD.5.geno
+
+"""
+
+import json
+import os
+import sys
+from typing import List
+
+import MySQLdb
+
+def conn():
+ return MySQLdb.Connect(db=os.environ.get("DB_NAME"),
+ user=os.environ.get("DB_USER"),
+ passwd=os.environ.get("DB_PASS"),
+ host=os.environ.get("DB_HOST"))
+
+def main(args):
+
+ # Directory in which .geno files are located
+ geno_dir = args[1]
+
+ # Directory in which to output new files
+ out_dir = args[2]
+
+ # The individuals group that we want to generate a .geno file for
+ target_file = geno_dir + args[3]
+
+ # The source group(s) we're generating the .geno files from
+ # This can be passed as either a specific .geno file (or set of files as multiple arguments),
+ # or as a JSON file containing a set of .geno files (and their corresponding file names and sample lists)
+ geno_json = {}
+ source_files = []
+ if ".json" in args[4]:
+ geno_json = json.load(open(geno_dir + args[4], "r"))
+ par_f1s = {
+ "mat": geno_json['mat'],
+ "pat": geno_json['pat'],
+ "f1s": geno_json['f1s']
+ }
+
+ # List of file titles and locations from JSON
+ source_files = [{'title': genofile['title'], 'location': geno_dir + genofile['location']} for genofile in geno_json['genofile']]
+ else:
+ par_f1s = {}
+ # List of files directly taken from command line arguments, with titles just set to the filename
+ for group in args[4:]:
+ file_name = geno_dir + group + ".geno" if ".geno" not in group else group
+ source_files.append({'title': file_name[:-5], 'location': file_name})
+
+ if len(source_files) > 1:
+ # Generate a JSON file pointing to the new target genotype files, in situations where there are multiple source .geno files
+ target_json_loc = out_dir + ".".join(args[3].split(".")[:-1]) + ".json"
+ target_json = {'genofile': []}
+
+ # Generate the output .geno files
+ for source_file in source_files:
+ filename, samples = generate_new_genofile(source_file['location'], target_file, par_f1s, out_dir)
+
+ target_json['genofile'].append({
+ 'location': filename.split("/")[-1],
+ 'title': source_file['title'],
+ 'sample_list': samples
+ })
+
+ json.dump(target_json, open(target_json_loc, "w"))
+
+def get_strain_for_sample(sample):
+ query = (
+ "SELECT CaseAttributeXRefNew.Value "
+ "FROM CaseAttributeXRefNew, Strain "
+ "WHERE CaseAttributeXRefNew.CaseAttributeId=11 "
+ "AND CaseAttributeXRefNew.StrainId = Strain.Id "
+ "AND Strain.Name = %(name)s" )
+
+ with conn().cursor() as cursor:
+ cursor.execute(query, {"name": sample.strip()})
+ return cursor.fetchone()[0]
+
+def generate_new_genofile(source_genofile, target_genofile, par_f1s, out_dir):
+ source_samples = group_samples(source_genofile)
+ source_genotypes = strain_genotypes(source_genofile)
+ target_samples = group_samples(target_genofile)
+ strain_pos_map = map_strain_pos_to_target_group(source_samples, target_samples, par_f1s)
+
+ if len(source_genofile.split("/")[-1].split(".")) > 2:
+ # The number in the source genofile; for example 4 in BXD.4.geno
+ source_num = source_genofile.split("/")[-1].split(".")[-2]
+ target_filename = ".".join(target_genofile.split("/")[-1].split(".")[:-1]) + "." + source_num + ".geno"
+ else:
+ target_filename = ".".join(target_genofile.split("/")[-1].split(".")[:-1]) + ".geno"
+
+ file_location = out_dir + target_filename
+
+ with open(file_location, "w") as fh:
+ for metadata in ["name", "type", "mat", "pat", "het", "unk"]:
+ fh.write("@" + metadata + ":" + source_genotypes[metadata] + "\n")
+
+ header_line = ["Chr", "Locus", "cM", "Mb"] + target_samples
+ fh.write("\t".join(header_line))
+
+ for marker in source_genotypes['markers']:
+ line_items = [
+ marker['Chr'],
+ marker['Locus'],
+ marker['cM'],
+ marker['Mb']
+ ]
+
+ for pos in strain_pos_map:
+ if isinstance(pos, int):
+ line_items.append(marker['genotypes'][pos])
+ else:
+ if pos in ["mat", "pat"]:
+ line_items.append(source_genotypes[pos])
+ elif pos == "f1s":
+ line_items.append("H")
+ else:
+ line_items.append("U")
+
+ fh.write("\t".join(line_items) + "\n")
+
+ return file_location, target_samples
+
+def map_strain_pos_to_target_group(source_samples, target_samples, par_f1s):
+ """
+ Retrieve corresponding strain position for each sample in the target group
+
+ This is so the genotypes from the base genofile can be mapped to the samples in the target group
+
+ For example:
+ Base strains: BXD1, BXD2, BXD3
+ Target samples: BXD1_1, BXD1_2, BXD2_1, BXD3_1, BXD3_2, BXD3_3
+ Returns: [0, 0, 1, 2, 2, 2]
+ """
+ pos_map = []
+ for sample in target_samples:
+ sample_strain = get_strain_for_sample(sample)
+ if sample_strain in source_samples:
+ pos_map.append(source_samples.index(sample_strain))
+ else:
+ val = "U"
+ for key in par_f1s.keys():
+ if sample_strain in par_f1s[key]:
+ val = key
+ pos_map.append(val)
+
+ return pos_map
+
+def group_samples(target_file: str) -> List:
+ """
+ Get the group samples from its "dummy" .geno file (which still contains the sample list)
+ """
+
+ sample_list = []
+ with open(target_file, "r") as target_geno:
+ for i, line in enumerate(target_geno):
+ # Skip header lines
+ if line[0] in ["#", "@"] or not len(line):
+ continue
+
+ line_items = line.split("\t")
+ sample_list = [item for item in line_items if item not in ["Chr", "Locus", "Mb", "cM"]]
+ break
+
+ return sample_list
+
+def strain_genotypes(strain_genofile: str) -> List:
+ """
+ Read genotypes from source strain .geno file
+
+ :param strain_genofile: string of genofile filename
+ :return: a list of dictionaries representing each marker's genotypes
+
+ Example output: [
+ {
+ 'Chr': '1',
+ 'Locus': 'marker1',
+ 'Mb': '10.0',
+ 'cM': '8.0',
+ 'genotypes': [('BXD1', 'B'), ('BXD2', 'D'), ('BXD3', 'H'), ...]
+ },
+ ...
+ ]
+ """
+
+ geno_dict = {}
+
+ geno_start_col = None
+ header_columns = []
+ sample_list = []
+ markers = []
+ with open(strain_genofile, "r") as source_geno:
+ for i, line in enumerate(source_geno):
+ if line[0] == "@":
+ metadata_type = line[1:].split(":")[0]
+ if metadata_type in ['name', 'type', 'mat', 'pat', 'het', 'unk']:
+ geno_dict[metadata_type] = line.split(":")[1].strip()
+
+ continue
+
+ # Skip other header lines
+ if line[0] == "#" or not len(line):
+ continue
+
+ line_items = line.split("\t")
+ if "Chr" in line_items: # Header row
+ # Get the first column index containing genotypes
+ header_columns = line_items
+ for j, item in enumerate(line_items):
+ if item not in ["Chr", "Locus", "Mb", "cM"]:
+ geno_start_col = j
+ break
+
+ sample_list = line_items[geno_start_col:]
+ if not geno_start_col:
+ print("Check .geno file - expected columns not found")
+ sys.exit()
+ else: # Marker rows
+ this_marker = {
+ 'Chr': line_items[header_columns.index("Chr")],
+ 'Locus': line_items[header_columns.index("Locus")],
+ 'Mb': line_items[header_columns.index("Mb")],
+ 'cM': line_items[header_columns.index("cM")],
+ 'genotypes': [item.strip() for item in line_items][geno_start_col:]
+ }
+
+ markers.append(this_marker)
+
+ geno_dict['markers'] = markers
+
+ return geno_dict
+
+if __name__ == "__main__":
+ main(sys.argv)
+