Add summary subcommand.

* pyhegp/pyhegp.py: Import Summary and write_summary from
pyhegp.serialization.
(summary): New function.

1 files changed, 15 insertions, 0 deletions

diff --git a/pyhegp/pyhegp.py b/pyhegp/pyhegp.py
index 54b6bb9..8075f07 100644
--- a/pyhegp/pyhegp.py
+++ b/pyhegp/pyhegp.py
@@ -20,6 +20,8 @@ import click
 import numpy as np
 from scipy.stats import special_ortho_group
 
+from pyhegp.serialization import Summary, write_summary
+
 def random_key(rng, n):
     return special_ortho_group.rvs(n, random_state=rng)
 
@@ -45,6 +47,19 @@ def main():
 
 @main.command()
 @click.argument("genotype-file", type=click.File("r"))
+@click.option("--output", "-o", "summary_file",
+              type=click.File("wb"),
+              default="-",
+              help="output file")
+def summary(genotype_file, summary_file):
+    genotype = read_genotype(genotype_file)
+    write_summary(summary_file,
+                  Summary(genotype.shape[0],
+                          np.mean(genotype, axis=0),
+                          np.std(genotype, axis=0)))
+
+@main.command()
+@click.argument("genotype-file", type=click.File("r"))
 @click.argument("maf-file", type=click.File("r"))
 @click.argument("key-path", type=click.Path())
 @click.argument("ciphertext-path", type=click.Path())