reconfigure repo file tree

jass_preprocessing/jass_preprocessing/__init__.py → jass_preprocessing/__init__.py

@@ -6,13 +6,13 @@
     map_gwas
     dna_utils
     map_reference
-    compute
+    compute_score
     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
+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

jass_preprocessing/doc/Makefile

-# 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)

jass_preprocessing/doc/source/_autosummary/jass_preprocessing.compute_score.rst

-jass\_preprocessing.compute\_score package
-==========================================
-
-Module contents
----------------
-
-.. automodule:: jass_preprocessing.compute_score
-    :members:
-    :undoc-members:
-    :show-inheritance:

jass_preprocessing/doc/source/_autosummary/jass_preprocessing.dna_utils.rst

-jass\_preprocessing.dna\_utils package
-======================================
-
-Module contents
----------------
-
-.. automodule:: jass_preprocessing.dna_utils
-    :members:
-    :undoc-members:
-    :show-inheritance:

jass_preprocessing/doc/source/_autosummary/jass_preprocessing.map_gwas.rst

-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:

jass_preprocessing/doc/source/_autosummary/jass_preprocessing.map_reference.rst

-jass\_preprocessing.map\_reference package
-==========================================
-
-Module contents
----------------
-
-.. automodule:: jass_preprocessing.map_reference
-    :members:
-    :undoc-members:
-    :show-inheritance:

jass_preprocessing/doc/source/_autosummary/jass_preprocessing.rst

-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:

jass_preprocessing/doc/source/_autosummary/jass_preprocessing.save_output.rst

-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:

jass_preprocessing/doc/source/_autosummary/modules.rst

-jass_preprocessing
-==================
-
-.. toctree::
-   :maxdepth: 4
-
-   jass_preprocessing
-   setup

jass_preprocessing/doc/source/conf.py

-# -*- 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

jass_preprocessing/doc/source/index.rst

-.. 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`