diff options
| -rw-r--r-- | wqflask/maintenance/gen_ind_genofiles.py | 41 |
1 files changed, 35 insertions, 6 deletions
diff --git a/wqflask/maintenance/gen_ind_genofiles.py b/wqflask/maintenance/gen_ind_genofiles.py index b781d7d1..9a97626d 100644 --- a/wqflask/maintenance/gen_ind_genofiles.py +++ b/wqflask/maintenance/gen_ind_genofiles.py @@ -33,9 +33,22 @@ def main(args): else: source_files = [geno_dir + group + ".geno" if ".geno" not in group else group for group in args[4:]] + 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 + args[3].split(".")[:-1] + ".json" + target_json = {'genofile': []} + # Generate the output .geno files for source_file in source_files: - generate_new_genofile(source_file, target_file) + filename, samples = generate_new_genofile(source_file, target_file) + + target_json['genofile'].append({ + 'location': filename.split("/")[-1], + 'title': filename.split("/")[-1], + 'sample_list': samples + }) + + json.dump(target_json, open(target_json_loc, "w")) def get_strain_for_sample(sample): query = ( @@ -67,7 +80,7 @@ def map_strain_pos_to_target_group(base_samples, target_samples): Returns: [0, 0, 1, 2, 2, 2] """ pos_map = [] - for i, sample in enumerate(target_samples): + for sample in target_samples: sample_strain = get_strain_for_sample(sample) pos_map.append(base_samples.index(sample_strain)) @@ -110,14 +123,28 @@ def strain_genotypes(strain_genofile: str) -> List: ] """ + geno_dict = {} + geno_start_col = None header_columns = [] sample_list = [] marker_genotypes = [] with open(file_location, "r") as source_geno: for i, line in enumerate(source_geno): - # Skip header lines - if line[0] in ["#", "@"] or not len(line): + if line[0] == "@": + if "@type" in line: + geno_dict['type'] = line.split(":")[1] + if "@mat" in line: + geno_dict['mat'] = line.split(":")[1] + elif "@pat" in line: + geno_dict['pat'] = line.split(":")[1] + elif "@het" in line: + geno_dict['het'] = line.split(":")[1] + elif "@unk" in line: + geno_dict['unk'] = line.split(":")[1] + + # Skip other header lines + if line[0] == "#" or not len(line): continue line_items = line.split("\t") @@ -140,11 +167,13 @@ def strain_genotypes(strain_genofile: str) -> List: 'Locus': line_items[header_columns.index("Locus")], 'Mb': line_items[header_columns.index("Mb")], 'cM': line_items[header_columns.index("cM")], - 'genotypes': list(zip(sample_list, [item.strip() for item in line_items][geno_start_col:])) + 'genotypes': [item.strip() for item in line_items][geno_start_col:] } marker_genotypes.append(this_marker) - return marker_genotypes + geno_dict['genotypes'] = marker_genotypes + + return geno_dict if __name__ == "__main__": print("command line arguments:\n\t%s" % sys.argv) |