diff options
| -rw-r--r-- | wqflask/maintenance/gen_ind_genofiles.py | 30 |
1 files changed, 17 insertions, 13 deletions
diff --git a/wqflask/maintenance/gen_ind_genofiles.py b/wqflask/maintenance/gen_ind_genofiles.py index 8b958efa..b755c648 100644 --- a/wqflask/maintenance/gen_ind_genofiles.py +++ b/wqflask/maintenance/gen_ind_genofiles.py @@ -58,7 +58,7 @@ def main(args): 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 + file_name = geno_dir + group + ".geno" if ".geno" not in group else geno_dir + group source_files.append({'title': file_name[:-5], 'location': file_name}) if len(source_files) > 1: @@ -66,17 +66,19 @@ def main(args): 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) + # 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 - }) + target_json['genofile'].append({ + 'location': filename.split("/")[-1], + 'title': source_file['title'], + 'sample_list': samples + }) - json.dump(target_json, open(target_json_loc, "w")) + json.dump(target_json, open(target_json_loc, "w")) + else: + filename, samples = generate_new_genofile(source_files[0]['location'], target_file, par_f1s, out_dir) def get_strain_for_sample(sample): query = ( @@ -88,7 +90,8 @@ def get_strain_for_sample(sample): with conn().cursor() as cursor: cursor.execute(query, {"name": sample.strip()}) - return cursor.fetchone()[0] + strain = cursor.fetchone()[0] + return strain def generate_new_genofile(source_genofile, target_genofile, par_f1s, out_dir): source_samples = group_samples(source_genofile) @@ -110,7 +113,7 @@ def generate_new_genofile(source_genofile, target_genofile, par_f1s, out_dir): fh.write("@" + metadata + ":" + source_genotypes[metadata] + "\n") header_line = ["Chr", "Locus", "cM", "Mb"] + target_samples - fh.write("\t".join(header_line)) + fh.write("\t".join(header_line) + "\n") for marker in source_genotypes['markers']: line_items = [ @@ -172,7 +175,8 @@ def group_samples(target_file: str) -> List: if line[0] in ["#", "@"] or not len(line): continue - line_items = line.split("\t") + line_items = line.split() + sample_list = [item for item in line_items if item not in ["Chr", "Locus", "Mb", "cM"]] break |