# 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__": print("command line arguments:\n\t%s" % sys.argv) main(sys.argv)