From 23fa59e292744b7f73b25c37e7b7020cc6fef8da Mon Sep 17 00:00:00 2001
From: hjulienne <hanna.julienne@gmail.com>
Date: Sat, 24 Nov 2018 10:56:25 +0000
Subject: [PATCH] reconfigure repo file tree
---
jass_preprocessing/__init__.py | 18 ++
.../__pycache__/__init__.cpython-35.pyc | Bin 0 -> 569 bytes
.../__pycache__/compute.cpython-35.pyc | Bin 0 -> 2315 bytes
.../__pycache__/compute_score.cpython-35.pyc | Bin 0 -> 2321 bytes
.../__pycache__/dna_utils.cpython-35.pyc | Bin 0 -> 759 bytes
.../__pycache__/map_gwas.cpython-35.pyc | Bin 0 -> 4472 bytes
.../__pycache__/map_reference.cpython-35.pyc | Bin 0 -> 4295 bytes
.../__pycache__/save_output.cpython-35.pyc | Bin 0 -> 1770 bytes
.../compute.py => compute_score.py} | 0
.../{jass_preprocessing => }/dna_utils.py | 0
jass_preprocessing/doc/Makefile | 20 ---
.../jass_preprocessing.compute_score.rst | 10 --
.../jass_preprocessing.dna_utils.rst | 10 --
.../jass_preprocessing.map_gwas.rst | 22 ---
.../jass_preprocessing.map_reference.rst | 10 --
.../_autosummary/jass_preprocessing.rst | 57 ------
.../jass_preprocessing.save_output.rst | 22 ---
.../doc/source/_autosummary/modules.rst | 8 -
jass_preprocessing/doc/source/conf.py | 169 ------------------
jass_preprocessing/doc/source/index.rst | 101 -----------
.../jass_preprocessing/__init__.py | 18 --
.../__pycache__/__init__.cpython-35.pyc | Bin 625 -> 0 bytes
.../{jass_preprocessing => }/map_gwas.py | 0
.../{jass_preprocessing => }/map_reference.py | 0
.../{jass_preprocessing => }/requirements.txt | 0
.../{jass_preprocessing => }/save_output.py | 0
.../main_preprocessing.py | 0
jass_preprocessing/setup.py => setup.py | 0
28 files changed, 18 insertions(+), 447 deletions(-)
create mode 100644 jass_preprocessing/__init__.py
create mode 100644 jass_preprocessing/__pycache__/__init__.cpython-35.pyc
create mode 100644 jass_preprocessing/__pycache__/compute.cpython-35.pyc
create mode 100644 jass_preprocessing/__pycache__/compute_score.cpython-35.pyc
create mode 100644 jass_preprocessing/__pycache__/dna_utils.cpython-35.pyc
create mode 100644 jass_preprocessing/__pycache__/map_gwas.cpython-35.pyc
create mode 100644 jass_preprocessing/__pycache__/map_reference.cpython-35.pyc
create mode 100644 jass_preprocessing/__pycache__/save_output.cpython-35.pyc
rename jass_preprocessing/{jass_preprocessing/compute.py => compute_score.py} (100%)
rename jass_preprocessing/{jass_preprocessing => }/dna_utils.py (100%)
delete mode 100644 jass_preprocessing/doc/Makefile
delete mode 100644 jass_preprocessing/doc/source/_autosummary/jass_preprocessing.compute_score.rst
delete mode 100644 jass_preprocessing/doc/source/_autosummary/jass_preprocessing.dna_utils.rst
delete mode 100644 jass_preprocessing/doc/source/_autosummary/jass_preprocessing.map_gwas.rst
delete mode 100644 jass_preprocessing/doc/source/_autosummary/jass_preprocessing.map_reference.rst
delete mode 100644 jass_preprocessing/doc/source/_autosummary/jass_preprocessing.rst
delete mode 100644 jass_preprocessing/doc/source/_autosummary/jass_preprocessing.save_output.rst
delete mode 100644 jass_preprocessing/doc/source/_autosummary/modules.rst
delete mode 100644 jass_preprocessing/doc/source/conf.py
delete mode 100644 jass_preprocessing/doc/source/index.rst
delete mode 100644 jass_preprocessing/jass_preprocessing/__init__.py
delete mode 100644 jass_preprocessing/jass_preprocessing/__pycache__/__init__.cpython-35.pyc
rename jass_preprocessing/{jass_preprocessing => }/map_gwas.py (100%)
rename jass_preprocessing/{jass_preprocessing => }/map_reference.py (100%)
rename jass_preprocessing/{jass_preprocessing => }/requirements.txt (100%)
rename jass_preprocessing/{jass_preprocessing => }/save_output.py (100%)
rename main_preprocessing.py => scripts/main_preprocessing.py (100%)
rename jass_preprocessing/setup.py => setup.py (100%)
diff --git a/jass_preprocessing/__init__.py b/jass_preprocessing/__init__.py
new file mode 100644
index 0000000..57bc151
--- /dev/null
+++ b/jass_preprocessing/__init__.py
@@ -0,0 +1,18 @@
+"""
+
+.. autosummary::
+ :toctree: _autosummary
+
+ map_gwas
+ dna_utils
+ map_reference
+ compute_score
+ save_output
+"""
+
+
+import jass_preprocessing.map_gwas
+import jass_preprocessing.dna_utils
+import jass_preprocessing.map_reference
+import jass_preprocessing.compute_score
+import jass_preprocessing.save_output
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diff --git a/jass_preprocessing/jass_preprocessing/compute.py b/jass_preprocessing/compute_score.py
similarity index 100%
rename from jass_preprocessing/jass_preprocessing/compute.py
rename to jass_preprocessing/compute_score.py
diff --git a/jass_preprocessing/jass_preprocessing/dna_utils.py b/jass_preprocessing/dna_utils.py
similarity index 100%
rename from jass_preprocessing/jass_preprocessing/dna_utils.py
rename to jass_preprocessing/dna_utils.py
diff --git a/jass_preprocessing/doc/Makefile b/jass_preprocessing/doc/Makefile
deleted file mode 100644
index e38284e..0000000
--- a/jass_preprocessing/doc/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# 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
deleted file mode 100644
index 5675ae5..0000000
--- a/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.compute_score.rst
+++ /dev/null
@@ -1,10 +0,0 @@
-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
deleted file mode 100644
index 7d55503..0000000
--- a/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.dna_utils.rst
+++ /dev/null
@@ -1,10 +0,0 @@
-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
deleted file mode 100644
index e48846f..0000000
--- a/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.map_gwas.rst
+++ /dev/null
@@ -1,22 +0,0 @@
-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
deleted file mode 100644
index 4d124a1..0000000
--- a/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.map_reference.rst
+++ /dev/null
@@ -1,10 +0,0 @@
-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
deleted file mode 100644
index 411912e..0000000
--- a/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.rst
+++ /dev/null
@@ -1,57 +0,0 @@
-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
deleted file mode 100644
index 08d580b..0000000
--- a/jass_preprocessing/doc/source/_autosummary/jass_preprocessing.save_output.rst
+++ /dev/null
@@ -1,22 +0,0 @@
-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
deleted file mode 100644
index 0f87917..0000000
--- a/jass_preprocessing/doc/source/_autosummary/modules.rst
+++ /dev/null
@@ -1,8 +0,0 @@
-jass_preprocessing
-==================
-
-.. toctree::
- :maxdepth: 4
-
- jass_preprocessing
- setup
diff --git a/jass_preprocessing/doc/source/conf.py b/jass_preprocessing/doc/source/conf.py
deleted file mode 100644
index a2e0a4c..0000000
--- a/jass_preprocessing/doc/source/conf.py
+++ /dev/null
@@ -1,169 +0,0 @@
-# -*- 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
deleted file mode 100644
index cee2dc0..0000000
--- a/jass_preprocessing/doc/source/index.rst
+++ /dev/null
@@ -1,101 +0,0 @@
-.. 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 JASS 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 |
-+----------+-------+------+-----+--------+
-
-Installation
-============
-
-In a folder that will contain the jass_preprocessing repository,
-execute the following lines:
-
-.. code-block:: shell
-
- git clone https://gitlab.pasteur.fr/statistical-genetics/JASS_Pre-processing.git
- cd JASS_Pre-processing/
- pip3 install ./jass_preprocessing/
-
-
-Preprocessing example
-=====================
-
-The file : "/JASS_Pre-processing/main_preprocessing.py" gives a complete example on
-how to use this package.
-
-
-Input
-======
-
-* A reference panel (1000 genome format). The user is expected to provide a reference panel in tsv format with the following columns in that order, without header:
-
-+-----+-----+------------+-----+-----+---------+
-| chr | pos | snp_id | ref | alt | MAF |
-+=====+=====+============+=====+=====+=========+
-| 1 |13116| rs62635286 | T | G |0.0970447|
-+-----+-----+------------+-----+-----+---------+
-| 1 |13118| rs200579949| A | G |0.0970447|
-+-----+-----+------------+-----+-----+---------+
-| 1 |14604| rs541940975| A | G | 0.147564|
-+-----+-----+------------+-----+-----+---------+
-| 1 |14930| rs75454623 | A | G | 0.482228|
-+-----+-----+------------+-----+-----+---------+
-
-* 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:
-
- * a header
- * 1 line per study
- * the fields are:
-
-
-+-------------------------------------------+------------------------------------------------------------+
-| category | field name |
-+===========================================+============================================================+
-| path to the data | filename |
-+-------------------------------------------+------------------------------------------------------------+
-| study info fields | consortia,outcome,fullName,type,Nsample,Ncase,Ncontrol,Nsnp|
-+-------------------------------------------+------------------------------------------------------------+
-| names of the header in the GWAS file | snpid,a1,a2,freq,pval,n,z,OR,se,code,imp,ncas,ncont |
-+-------------------------------------------+------------------------------------------------------------+
-
-.. | I don't know | altNcas,altNcont|
-
-
-* it must contain the following columns:
-
-Hard coded path (l.20-29 of JASS_Pre-processing/main_preprocessing.py)
-
-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
deleted file mode 100644
index 0068d9b..0000000
--- a/jass_preprocessing/jass_preprocessing/__init__.py
+++ /dev/null
@@ -1,18 +0,0 @@
-"""
-
-.. 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
deleted file mode 100644
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diff --git a/jass_preprocessing/jass_preprocessing/map_gwas.py b/jass_preprocessing/map_gwas.py
similarity index 100%
rename from jass_preprocessing/jass_preprocessing/map_gwas.py
rename to jass_preprocessing/map_gwas.py
diff --git a/jass_preprocessing/jass_preprocessing/map_reference.py b/jass_preprocessing/map_reference.py
similarity index 100%
rename from jass_preprocessing/jass_preprocessing/map_reference.py
rename to jass_preprocessing/map_reference.py
diff --git a/jass_preprocessing/jass_preprocessing/requirements.txt b/jass_preprocessing/requirements.txt
similarity index 100%
rename from jass_preprocessing/jass_preprocessing/requirements.txt
rename to jass_preprocessing/requirements.txt
diff --git a/jass_preprocessing/jass_preprocessing/save_output.py b/jass_preprocessing/save_output.py
similarity index 100%
rename from jass_preprocessing/jass_preprocessing/save_output.py
rename to jass_preprocessing/save_output.py
diff --git a/main_preprocessing.py b/scripts/main_preprocessing.py
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rename from main_preprocessing.py
rename to scripts/main_preprocessing.py
diff --git a/jass_preprocessing/setup.py b/setup.py
similarity index 100%
rename from jass_preprocessing/setup.py
rename to setup.py
--
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