From 5ab52154a5413f4e3c898e07aed924e34fbe75ae Mon Sep 17 00:00:00 2001
From: hanna julienne <hanna.julienne@pasteur.fr>
Date: Mon, 26 Mar 2018 17:27:22 +0200
Subject: [PATCH] adding main file
---
impute_jass/impute_jass/imputation_launcher.py | 12 ++++++++++++
impute_jass/impute_jass/main.py | 0
impute_jass/impute_jass/stat_models.py | 2 +-
impute_jass/setup.py | 12 ++++++------
4 files changed, 19 insertions(+), 7 deletions(-)
create mode 100644 impute_jass/impute_jass/main.py
diff --git a/impute_jass/impute_jass/imputation_launcher.py b/impute_jass/impute_jass/imputation_launcher.py
index e4ff662..97f487c 100644
--- a/impute_jass/impute_jass/imputation_launcher.py
+++ b/impute_jass/impute_jass/imputation_launcher.py
@@ -6,6 +6,18 @@ import glob
import pandas as pd
from .windows import ld_region_centered_window_imputation, impg_like_imputation, realigned_zfiles_on_panel
+
+def chromosome_imputation_entry_point(chrom, zscore, ref_panel, ld_folder, window_size=10000, imputation_style="online", buf=2500, lamb= 0.01, pinv_rcond = 0.01):
+ """
+ Function whose only purpose is to allow the calling of the ImputationLauncher.chromosome_imputation method
+ from an entry point
+ """
+ imputer = ImputationLauncher( window_size=10000, imputation_style="online", buf=2500, lamb= 0.01, pinv_rcond = 0.01)
+ imputer.chromosome_imputation(chrom, zscore, ref_panel, ld_folder)
+
+
+
+
class ImputationLauncher(object):
"""
Class perform imputation of snp from summary statistic
diff --git a/impute_jass/impute_jass/main.py b/impute_jass/impute_jass/main.py
new file mode 100644
index 0000000..e69de29
diff --git a/impute_jass/impute_jass/stat_models.py b/impute_jass/impute_jass/stat_models.py
index a9e9ea0..a5c5343 100644
--- a/impute_jass/impute_jass/stat_models.py
+++ b/impute_jass/impute_jass/stat_models.py
@@ -28,7 +28,7 @@ def impg_model(zt, sig_t, sig_i_t, lamb=0.01, rcond=0.01, batch=True):
"""
sig_t = sig_t.values
np.fill_diagonal(sig_t, (1+lamb))
- sig_t_inv = sc.linalg.pinv(sig_t)#, rcond=rcond)
+ sig_t_inv = sc.linalg.pinv(sig_t, rcond=rcond)
if batch:
condition_number = np.array([np.linalg.cond(sig_t)]*sig_i_t.shape[0])
diff --git a/impute_jass/setup.py b/impute_jass/setup.py
index 89c7c36..4ceebab 100644
--- a/impute_jass/setup.py
+++ b/impute_jass/setup.py
@@ -12,11 +12,11 @@ setup(name='impute_jass',
package_data = {'impute_jass':'./data/*.csv'},
zip_safe=False
- entry_points={
- 'console_scripts' : [
- 'impute_chromosome = '
-
- ]
- }
+ # entry_points={
+ # 'console_scripts' : [
+ # 'impute_chromosome = imputation_launcher:chromosome_imputation_entry_point'
+ #
+ # ]
+ # }
)
--
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