diff options
| -rw-r--r-- | pyhegp/pyhegp.py | 38 |
1 files changed, 30 insertions, 8 deletions
diff --git a/pyhegp/pyhegp.py b/pyhegp/pyhegp.py index 8217040..fcd20ea 100644 --- a/pyhegp/pyhegp.py +++ b/pyhegp/pyhegp.py @@ -26,7 +26,7 @@ import numpy as np import pandas as pd from scipy.stats import special_ortho_group -from pyhegp.serialization import Summary, read_summary, write_summary, read_genotype, write_genotype, write_key, is_genotype_metadata_column +from pyhegp.serialization import Summary, read_summary, write_summary, read_genotype, read_phenotype, write_genotype, write_phenotype, write_key, is_genotype_metadata_column Stats = namedtuple("Stats", "n mean std") @@ -110,13 +110,12 @@ def encrypt_genotype(genotype, key, summary): columns=sample_names)), axis="columns") -def cat_genotype(genotypes): - def cat2(genotype1, genotype2): - return pd.merge(genotype1, genotype2, - how="inner", - on=list(filter(is_genotype_metadata_column, - genotype1.columns))) +def cat_data_frames(frames, metadata_columns): + def cat2(df1, df2): + return pd.merge(df1, df2, how="inner", on=metadata_columns) + return reduce(cat2, frames) +def cat_genotype(genotypes): match genotypes: # If there are no input data frames, return an empty data # frame with the chromosome and position columns. @@ -127,7 +126,19 @@ def cat_genotype(genotypes): genotype.position = genotype.position.astype("int") return genotype case _: - return reduce(cat2, genotypes) + return cat_data_frames(genotypes, + list(filter(is_genotype_metadata_column, + genotypes[0].columns))) + +def cat_phenotype(phenotypes): + match phenotypes: + # If there are no input data frames, return an empty data + # frame with the sample-id column. + case []: + return pd.DataFrame(data={"sample-id": []}, + dtype="str") + case _: + return cat_data_frames(phenotypes, ["sample-id"]) @click.group() def main(): @@ -198,5 +209,16 @@ def cat_genotype_command(output_file, ciphertext_files): cat_genotype([read_genotype(file) for file in ciphertext_files])) +@main.command("cat-phenotype") +@click.option("--output", "-o", "output_file", + type=click.File("wb"), + default="-", + help="output file") +@click.argument("ciphertext-files", type=click.File("rb"), nargs=-1) +def cat_phenotype_command(output_file, ciphertext_files): + write_phenotype(output_file, + cat_phenotype([read_phenotype(file) + for file in ciphertext_files])) + if __name__ == "__main__": main() |