diff --git a/impute_jass/impute_jass/imputation_launcher.py b/impute_jass/impute_jass/imputation_launcher.py index e4ff6625cbd1a997640ff0b3cad3106adaf27f86..97f487ced4c01736a8e7e750e38ab9b50a6e4a6f 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 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/impute_jass/impute_jass/stat_models.py b/impute_jass/impute_jass/stat_models.py index a9e9ea02a815a7dc8fac43fc405a4e1d53ed5932..a5c5343e3bd920ece9aa1cd8f3494881772d62b6 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 89c7c36a49cf1f3fc3c069c224be3632b6ad3fcb..4ceebabd878f790b3d0aecec95831c651b28a443 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' + # + # ] + # } )