diff options
| -rw-r--r-- | wqflask/maintenance/gen_ind_genofiles.py | 29 |
1 files changed, 28 insertions, 1 deletions
diff --git a/wqflask/maintenance/gen_ind_genofiles.py b/wqflask/maintenance/gen_ind_genofiles.py index 6e818945..b91660a4 100644 --- a/wqflask/maintenance/gen_ind_genofiles.py +++ b/wqflask/maintenance/gen_ind_genofiles.py @@ -28,7 +28,7 @@ def main(args): target_groups = [args[2]] # Generate the output .geno files - generate_new_genofiles(strain_genotypes(source_genofile), target_groups) + generate_new_genofiles(source_genofile, strain_genotypes(source_genofile), target_groups) def get_strain_for_sample(sample): query = ( @@ -41,6 +41,33 @@ def get_strain_for_sample(sample): with conn.cursor() as cursor: return cursor.execute(query, {"name": name}).fetchone()[0] +def generate_new_genofiles(source_genofile, strain_genotypes, target_groups): + for group in target_groups: + base_samples = group_samples(source_genofile) + target_samples = group_samples(group) + strain_pos_map = map_strain_pos_to_target_group(base_samples, target_samples) + + new_genofile = app.config.get("GENENETWORK_FILES") + "/genotype/_" + group + + +def map_strain_pos_to_target_group(base_samples, target_samples): + """ + 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 i, sample in enumerate(target_samples): + sample_strain = get_strain_for_sample(sample) + pos_map.append(base_samples.index(sample_strain)) + + return pos_map + def group_samples(target_group: str) -> List: """ Get the group samples from its "dummy" .geno file (which still contains the sample list) |