From d561f244850a4e909ce41a5d92cd6f828d1daeaf Mon Sep 17 00:00:00 2001
From: hjulienne <hanna.julienne@gmail.com>
Date: Thu, 22 Feb 2018 19:42:55 +0100
Subject: [PATCH] fix module structure
---
.../jass_preprocessing/__init__.py | 4 ++--
.../jass_preprocessing/dna_utils/__init__.py | 0
.../jass_preprocessing/map_gwas/__init__.py | 0
.../map_gwas/__pycache__/map_gwas.cpython-35.pyc | Bin 576 -> 0 bytes
.../jass_preprocessing/map_gwas/map_gwas.py | 15 ++++++++++++++-
5 files changed, 16 insertions(+), 3 deletions(-)
create mode 100644 jass_preprocessing/jass_preprocessing/dna_utils/__init__.py
create mode 100644 jass_preprocessing/jass_preprocessing/map_gwas/__init__.py
delete mode 100644 jass_preprocessing/jass_preprocessing/map_gwas/__pycache__/map_gwas.cpython-35.pyc
diff --git a/jass_preprocessing/jass_preprocessing/__init__.py b/jass_preprocessing/jass_preprocessing/__init__.py
index 8669fc7..fcd7f03 100644
--- a/jass_preprocessing/jass_preprocessing/__init__.py
+++ b/jass_preprocessing/jass_preprocessing/__init__.py
@@ -1,2 +1,2 @@
-import jass_preprocessing.map_gwas.map_gwas
-import jass_preprocessing.dna_utils.dna_utils
+import jass_preprocessing.map_gwas
+import jass_preprocessing.dna_utils
diff --git a/jass_preprocessing/jass_preprocessing/dna_utils/__init__.py b/jass_preprocessing/jass_preprocessing/dna_utils/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/jass_preprocessing/jass_preprocessing/map_gwas/__init__.py b/jass_preprocessing/jass_preprocessing/map_gwas/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/jass_preprocessing/jass_preprocessing/map_gwas/__pycache__/map_gwas.cpython-35.pyc b/jass_preprocessing/jass_preprocessing/map_gwas/__pycache__/map_gwas.cpython-35.pyc
deleted file mode 100644
index a080559f1ba2ed9e2ae37219fc43f4397bf6141d..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/jass_preprocessing/jass_preprocessing/map_gwas/map_gwas.py b/jass_preprocessing/jass_preprocessing/map_gwas/map_gwas.py
index aef00bb..2becf22 100644
--- a/jass_preprocessing/jass_preprocessing/map_gwas/map_gwas.py
+++ b/jass_preprocessing/jass_preprocessing/map_gwas/map_gwas.py
@@ -1,6 +1,6 @@
import os
import sys
-
+import pandas as pd
@@ -29,3 +29,16 @@ def gwas_internal_link(GWAS_table, GWAS_path):
'internalDataLink': walkfs(GWAS_path, GWAS_filename)[2]})
Glink = pd.DataFrame(Glink, columns=('filename', 'internalDataLink'))
return Glink
+
+
+def convert_missing_values(df):
+ """
+ Convert all missing value strings to a standart np.nan value
+ """
+ def_missing = ['', '#N/A', '#N/A', 'N/A', '#NA', '-1.#IND', '-1.#QNAN', '-NaN',
+ '-nan', '1.#IND', '1.#QNAN', 'N/A', 'NA', 'NULL', 'NaN', 'nan', 'na', '.']
+
+ nmissing = len(def_missing)
+ nan_vec = [np.nan] * nmissing
+
+ return df.replace(def_missing, nan_vec)
--
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