diff --git a/jass_preprocessing/doc/Makefile b/jass_preprocessing/doc/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..e38284eb08079a3ae55eaf7c81f3e81335243ed0
--- /dev/null
+++ b/jass_preprocessing/doc/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+SPHINXPROJ = jass_preprocessing
+SOURCEDIR = source
+BUILDDIR = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.compute_score.rst b/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.compute_score.rst
new file mode 100644
index 0000000000000000000000000000000000000000..5675ae5918779cf7f1dc67820117f429ad6e681a
--- /dev/null
+++ b/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.compute_score.rst
@@ -0,0 +1,10 @@
+jass\_preprocessing.compute\_score package
+==========================================
+
+Module contents
+---------------
+
+.. automodule:: jass_preprocessing.compute_score
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.dna_utils.rst b/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.dna_utils.rst
new file mode 100644
index 0000000000000000000000000000000000000000..7d555035def45128c2148a9c81ada2c85edfcc28
--- /dev/null
+++ b/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.dna_utils.rst
@@ -0,0 +1,10 @@
+jass\_preprocessing.dna\_utils package
+======================================
+
+Module contents
+---------------
+
+.. automodule:: jass_preprocessing.dna_utils
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.map_gwas.rst b/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.map_gwas.rst
new file mode 100644
index 0000000000000000000000000000000000000000..e48846fd9d2d032c3a196c29a2d5e83b3d0c461e
--- /dev/null
+++ b/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.map_gwas.rst
@@ -0,0 +1,22 @@
+jass\_preprocessing.map\_gwas package
+=====================================
+
+Submodules
+----------
+
+jass\_preprocessing.map\_gwas.map\_gwas module
+----------------------------------------------
+
+.. automodule:: jass_preprocessing.map_gwas.map_gwas
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: jass_preprocessing.map_gwas
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.map_reference.rst b/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.map_reference.rst
new file mode 100644
index 0000000000000000000000000000000000000000..4d124a13b4553c6f820fd9997008477c048b9deb
--- /dev/null
+++ b/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.map_reference.rst
@@ -0,0 +1,10 @@
+jass\_preprocessing.map\_reference package
+==========================================
+
+Module contents
+---------------
+
+.. automodule:: jass_preprocessing.map_reference
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.rst b/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.rst
new file mode 100644
index 0000000000000000000000000000000000000000..411912e411c26de2c1709c4a2128c8fc5fae72b1
--- /dev/null
+++ b/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.rst
@@ -0,0 +1,57 @@
+jass\_preprocessing package
+===========================
+
+Subpackages
+-----------
+
+.. toctree::
+
+ jass_preprocessing.compute_score
+ jass_preprocessing.dna_utils
+ jass_preprocessing.map_gwas
+ jass_preprocessing.map_reference
+ jass_preprocessing.save_output
+
+Submodules
+----------
+
+jass\_preprocessing.compute module
+----------------------------------
+
+.. automodule:: jass_preprocessing.compute
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+jass\_preprocessing.dna\_utils module
+-------------------------------------
+
+.. automodule:: jass_preprocessing.dna_utils
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+jass\_preprocessing.map\_gwas module
+------------------------------------
+
+.. automodule:: jass_preprocessing.map_gwas
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+jass\_preprocessing.map\_reference module
+-----------------------------------------
+
+.. automodule:: jass_preprocessing.map_reference
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: jass_preprocessing
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.save_output.rst b/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.save_output.rst
new file mode 100644
index 0000000000000000000000000000000000000000..08d580ba7a12118e142d658cbf420308cdace1ff
--- /dev/null
+++ b/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.save_output.rst
@@ -0,0 +1,22 @@
+jass\_preprocessing.save\_output package
+========================================
+
+Submodules
+----------
+
+jass\_preprocessing.save\_output.save\_output module
+----------------------------------------------------
+
+.. automodule:: jass_preprocessing.save_output.save_output
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: jass_preprocessing.save_output
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/jass_preprocessing/doc/source/_autosummary/modules.rst b/jass_preprocessing/doc/source/_autosummary/modules.rst
new file mode 100644
index 0000000000000000000000000000000000000000..0f879179dc2ae72831eb20cb665b174f19db2688
--- /dev/null
+++ b/jass_preprocessing/doc/source/_autosummary/modules.rst
@@ -0,0 +1,8 @@
+jass_preprocessing
+==================
+
+.. toctree::
+ :maxdepth: 4
+
+ jass_preprocessing
+ setup
diff --git a/jass_preprocessing/doc/source/conf.py b/jass_preprocessing/doc/source/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..a2e0a4c9b1e16179b91ba357bf91a65b46bf68e2
--- /dev/null
+++ b/jass_preprocessing/doc/source/conf.py
@@ -0,0 +1,169 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../../jass_preprocessing/'))
+
+# -- Project information -----------------------------------------------------
+
+project = 'jass_preprocessing'
+copyright = '2018, Hanna Julienne'
+author = 'Hanna Julienne'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = '1.0'
+
+# -- General configuration ---------------------------------------------------
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+ 'sphinx.ext.autodoc',
+ 'sphinx.ext.napoleon',
+ 'sphinx.ext.coverage',
+ 'sphinx.ext.mathjax',
+ 'sphinx.ext.viewcode',
+ 'sphinx.ext.todo',
+ 'sphinx.ext.coverage'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path .
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'bizstyle'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself. Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'jass_preprocessingdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+ # The paper size ('letterpaper' or 'a4paper').
+ #
+ # 'papersize': 'letterpaper',
+
+ # The font size ('10pt', '11pt' or '12pt').
+ #
+ # 'pointsize': '10pt',
+
+ # Additional stuff for the LaTeX preamble.
+ #
+ # 'preamble': '',
+
+ # Latex figure (float) alignment
+ #
+ # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+# author, documentclass [howto, manual, or own class]).
+latex_documents = [
+ (master_doc, 'jass_preprocessing.tex',
+ 'jass\\_preprocessing Documentation',
+ 'Hanna Julienne', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ (master_doc, 'jass_preprocessing', 'jass_preprocessing Documentation',
+ [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ (master_doc, 'jass_preprocessing', 'jass_preprocessing Documentation',
+ author, 'jass_preprocessing', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
diff --git a/jass_preprocessing/doc/source/index.rst b/jass_preprocessing/doc/source/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..f214866ce0e7a184405e932519f9a91aa8d4c86b
--- /dev/null
+++ b/jass_preprocessing/doc/source/index.rst
@@ -0,0 +1,55 @@
+.. jass_preprocessing documentation master file, created by
+ sphinx-quickstart on Wed Nov 7 11:03:55 2018.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to jass_preprocessing's documentation!
+==============================================
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+
+What is jass preprocessing ?
+============================
+Jass preprocessing is a tool package that take in input
+heterogeneous GWAS summary statistics and perform standardization and quality
+checks to output standardize summary statistic files that can be used as input
+in the JAS S python package and the RAISS imputation package.
+
+The QC and preprocessing step goes as follow:
+
+* map column from of a specific GWAS to standardize names
+* Select GWAS SNPs that are in the input reference panel
+* Align coded allele of the GWAS with the reference panel
+* Save the output by chromosome as the following example:
+
++----------+-------+------+-----+--------+
+| rsID | pos | A0 | A1 | Z |
++==========+=======+======+=====+========+
+| rs6548219| 30762 | A | G | -1.133 |
++----------+-------+------+-----+--------+
+
+Preprocessing example
+=====================
+
+The file : "/JASS_Pre-processing/main_preprocessing.py" gives an example on how to use
+this package.
+
+
+Input
+======
+
+* A reference panel (1000 genome format)
+* Folder containing all raw gwas data (all chromosomes in one file)
+* a list containing the name of GWAS file to the string format.
+* A descriptor csv files that will described each GWAS summary statistic files
+* it must contain the following columns:
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/jass_preprocessing/jass_preprocessing/__init__.py b/jass_preprocessing/jass_preprocessing/__init__.py
index dd0779d4736d3bef5c788138c31b9fe4a720240a..0068d9b9f103f45786e58e5cf6cea7585e19e797 100644
--- a/jass_preprocessing/jass_preprocessing/__init__.py
+++ b/jass_preprocessing/jass_preprocessing/__init__.py
@@ -1,5 +1,18 @@
-import jass_preprocessing.map_gwas.map_gwas as map_gwas
-import jass_preprocessing.dna_utils.dna_utils as dna_utils
-import jass_preprocessing.map_reference.map_reference as map_reference
-import jass_preprocessing.compute_score.compute as compute_score
-import jass_preprocessing.save_output.save_output as save_output
+"""
+
+.. autosummary::
+ :toctree: _autosummary
+
+ map_gwas
+ dna_utils
+ map_reference
+ compute
+ save_output
+"""
+
+
+import jass_preprocessing.map_gwas as map_gwas
+import jass_preprocessing.dna_utils as dna_utils
+import jass_preprocessing.map_reference as map_reference
+import jass_preprocessing.compute as compute_score
+import jass_preprocessing.save_output as save_output
diff --git a/jass_preprocessing/jass_preprocessing/__pycache__/__init__.cpython-35.pyc b/jass_preprocessing/jass_preprocessing/__pycache__/__init__.cpython-35.pyc
index 6590be3001f7e28dd83d3108b92080eb83379f31..27038cd7cd2b8bc45adef0e8559bfb6bc41a8d97 100644
Binary files a/jass_preprocessing/jass_preprocessing/__pycache__/__init__.cpython-35.pyc and b/jass_preprocessing/jass_preprocessing/__pycache__/__init__.cpython-35.pyc differ
diff --git a/jass_preprocessing/jass_preprocessing/compute_score/compute.py b/jass_preprocessing/jass_preprocessing/compute.py
similarity index 100%
rename from jass_preprocessing/jass_preprocessing/compute_score/compute.py
rename to jass_preprocessing/jass_preprocessing/compute.py
diff --git a/jass_preprocessing/jass_preprocessing/compute_score/__init__.py b/jass_preprocessing/jass_preprocessing/compute_score/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/jass_preprocessing/jass_preprocessing/dna_utils/dna_utils.py b/jass_preprocessing/jass_preprocessing/dna_utils.py
similarity index 100%
rename from jass_preprocessing/jass_preprocessing/dna_utils/dna_utils.py
rename to jass_preprocessing/jass_preprocessing/dna_utils.py
diff --git a/jass_preprocessing/jass_preprocessing/dna_utils/__init__.py b/jass_preprocessing/jass_preprocessing/dna_utils/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/jass_preprocessing/jass_preprocessing/map_gwas/map_gwas.py b/jass_preprocessing/jass_preprocessing/map_gwas.py
similarity index 66%
rename from jass_preprocessing/jass_preprocessing/map_gwas/map_gwas.py
rename to jass_preprocessing/jass_preprocessing/map_gwas.py
index b906d03c807a6d92a05ceda24a81c25d131fcfa2..2b0816f39f27a12c3214d0313c69cef626e3fcda 100644
--- a/jass_preprocessing/jass_preprocessing/map_gwas/map_gwas.py
+++ b/jass_preprocessing/jass_preprocessing/map_gwas.py
@@ -1,9 +1,25 @@
+"""
+Map GWAS
+
+A set of functions to find GWAS files in subfolder and
+to map columns
+
+"""
+
import os
import sys
import pandas as pd
import numpy as np
def walkfs(startdir, findfile):
+ """
+
+ Go through the folder and subfolder to find the specified file
+
+ Args:
+ startdir (str): path of the folder to explore
+ findfile (str): name of the file to find
+ """
dircount = 0
filecount = 0
for root, dirs, files in os.walk(startdir):
@@ -18,6 +34,15 @@ def walkfs(startdir, findfile):
def gwas_internal_link(GWAS_table, GWAS_path):
"""
Walk the GWAS path to find the GWAS tables
+
+ Args:
+ GWAS_table (str): path of the folder to explore
+ findfile (str): name of the file to find
+
+ Return:
+ a pandas dataframe with one column for the filename
+ and one column containing the complete path to the file
+
"""
Glink = []
@@ -32,6 +57,11 @@ def gwas_internal_link(GWAS_table, GWAS_path):
def convert_missing_values(df):
"""
Convert all missing value strings to a standart np.nan value
+
+ Args:
+ GWAS_table (pandas dataframe): GWAS data as a dataframe
+ Return:
+ a pandas dataframe with missing value all equal to np.nan
"""
def_missing = ['', '#N/A', '#N/A', 'N/A', '#NA', '-1.#IND', '-1.#QNAN',
'-NaN',
@@ -46,13 +76,20 @@ def convert_missing_values(df):
def map_columns_position(gwas_internal_link, GWAS_labels):
"""
Find column position for each specific Gwas
+
+ Args:
+ gwas_internal_link (str): filename of the GWAS data (with path)
+ GWAS_labels (str): filename of the csv information file
+
+ Return:
+ pandas Series with column position and column names as index
"""
column_dict = pd.read_csv(GWAS_labels, sep='\t', na_values='na', index_col=0)
gwas_file = gwas_internal_link.split('/')[-1]
my_labels = column_dict.loc[gwas_file]
- column_dict.head()
+
#Our standart labels:
reference_label = column_dict.columns.tolist()
# labels in the GWAS files
@@ -81,16 +118,26 @@ def map_columns_position(gwas_internal_link, GWAS_labels):
def read_gwas( gwas_internal_link, column_map):
"""
- Read gwas Chromosome and rename columns in our standart
+ Read gwas raw data, fetch columns thanks to position stored in
+ column_map and rename columns according to column_map.index
+
+ Args:
+ gwas_internal_link (str): GWAS data as a dataframe
+ column_map (pandas Series): Series containing the position of column in
+ the raw data
+ Return:
+ a pandas dataframe with missing value all equal to np.nan
"""
fullGWAS = pd.read_csv(gwas_internal_link, delim_whitespace=True,
usecols = column_map.values, #column_dict['label_position'].keys(),
names= column_map.index,
index_col=0,
- header=0, na_values= ['', '#N/A', '#N/A', 'N/A', '#NA', '-1.#IND', '-1.#QNAN',
+ header=0, na_values= ['', '#N/A', '#N/A', 'N/A',
+ '#NA', '-1.#IND', '-1.#QNAN',
'-NaN',
- '-nan', '1.#IND', '1.#QNAN', 'N/A', 'NA', 'NULL', 'NaN',
+ '-nan', '1.#IND', '1.#QNAN', 'N/A',
+ 'NA', 'NULL', 'NaN',
'nan', 'na', '.'])
fullGWAS = fullGWAS[~fullGWAS.index.duplicated(keep='first')]
diff --git a/jass_preprocessing/jass_preprocessing/map_gwas/__init__.py b/jass_preprocessing/jass_preprocessing/map_gwas/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/jass_preprocessing/jass_preprocessing/map_reference/map_reference.py b/jass_preprocessing/jass_preprocessing/map_reference.py
similarity index 100%
rename from jass_preprocessing/jass_preprocessing/map_reference/map_reference.py
rename to jass_preprocessing/jass_preprocessing/map_reference.py
diff --git a/jass_preprocessing/jass_preprocessing/map_reference/__init__.py b/jass_preprocessing/jass_preprocessing/map_reference/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/jass_preprocessing/jass_preprocessing/save_output/save_output.py b/jass_preprocessing/jass_preprocessing/save_output.py
similarity index 100%
rename from jass_preprocessing/jass_preprocessing/save_output/save_output.py
rename to jass_preprocessing/jass_preprocessing/save_output.py
diff --git a/jass_preprocessing/jass_preprocessing/save_output/__init__.py b/jass_preprocessing/jass_preprocessing/save_output/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/jass_preprocessing/setup.py b/jass_preprocessing/setup.py
index 5e11bb38e0bf3c14d3ad782a95c0b918519d46bb..748c456d9197b6b7cdbb5ac70b49c8967b3c5efa 100644
--- a/jass_preprocessing/setup.py
+++ b/jass_preprocessing/setup.py
@@ -2,14 +2,13 @@ from setuptools import setup, find_packages
setup(name='jass_preprocessing',
version='0.1',
- description='Preprocess GWAS summary statistic for JASS',
+ description='Preprocess and standardize heterogeneous GWAS summary statistic for JASS',
url='http:https://gitlab.pasteur.fr/statistical-genetics/JASS_Pre-processing',
author='Hugues Aschard, Hanna Julienne, Vincent Laville',
author_email='hugues.aschard@pasteur.fr',
license='MIT',
#package_dir = {'': 'jass_preprocessing'},
- packages= ['jass_preprocessing', "jass_preprocessing.map_gwas",
- "jass_preprocessing.dna_utils", "jass_preprocessing.map_reference",
- "jass_preprocessing.compute_score", "jass_preprocessing.save_output"
- ],
+ packages= ['jass_preprocessing'],
zip_safe=False)
+
+#, "jass_preprocessing.map_gwas","jass_preprocessing.dna_utils", "jass_preprocessing.map_reference","jass_preprocessing.compute_score", "jass_preprocessing.save_output"
diff --git a/main_preprocessing.py b/main_preprocessing.py
index e4248c2ae2c652334a9fd78f27888731aa9dce28..d95a03439986bd84e0edf04bd98c2d5b1465fd36 100644
--- a/main_preprocessing.py
+++ b/main_preprocessing.py
@@ -1,6 +1,6 @@
"""
Read raw GWAS summary statistics, filter and format
-Write clean GWAS
+Write clean GWAS datasets by chromosome
"""
__updated__ = '2018-26-06'
@@ -27,8 +27,10 @@ REF_filename = netPath+'PCMA/0._REF/1KGENOME/summary_genome_Filter_part2.out'
pathOUT = netPath+'PCMA/1._DATA/RAW.summary/'
ImpG_output_Folder = netPath+ 'PCMA/1._DATA/preprocessing_test/'
+
+# Read the information on GWAS file and set the gwas file name as index:
+
gwas_map = pd.read_csv(GWAS_labels, sep="\t", index_col=0)
-gwas_map
#GWAS_table = gwas_map.index[22:]#["GIANT_2015_HIP_COMBINED_EUR.txt"]#"EUR.CD.gwas_filtered.assoc"]
#GWAS_table[5:]
# "GWAS_DBP_recoded.txt","GWAS_MAP_recoded.txt", #"GWAS_SBP_recoded_dummy.txt"
@@ -36,8 +38,8 @@ gwas_map
# "GIANT_2015_HIP_COMBINED_EUR.txt",
# ]
-gwas_map
GWAS_table = ["Menopause_HapMap_for_website_18112015.txt"] # gwas_map.index#["gabriel_asthma_dummy.txt"]
+
for GWAS_filename in GWAS_table:
tag = "{0}_{1}".format(gwas_map.loc[GWAS_filename, 'consortia'],
@@ -75,9 +77,3 @@ mgwas.head()
GWAS_labels
pd.read_csv(GWAS_labels, sep='\t', na_values='na', index_col=0)
-
-mapgw.head()
-
-GWAS_path
-GWAS_labels
-mapgw