initial commit

Author: AlexTISYoung

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) [2017] [Alexander Thomas Ian Strudwick Young]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MANIFEST.in

@@ -0,0 +1,2 @@
+include *.txt
+recursive-include docs *.txt

README.md

@@ -0,0 +1,47 @@
+# sibreg
+sibreg is a python library for performing robust GWAS using sibling pairs with a random effects
+model for within family phenotypic correlations
+
+
+# Main features:
+
+regrnd class: given data, find the parameters that maximise
+the likelihood and their sampling distribution.
+
+
+# Package Install Instructions
+
+sibreg has the following dependencies:
+
+python 2.7
+
+Packages: 
+
+- numpy
+- scipy
+- pysnptools
+
+We highly recommend using a python distribution such as Anaconda (https://store.continuum.io/cshop/anaconda/). 
+This will come with both numpy and scipy installed and can include an MKL-compiled distribution
+for optimal speed. 
+
+To install from source, clone the git repository, and in the directory
+containing the sibreg source code, at the shell type
+
+    'sudo python setupy.py install'
+
+or, on the windows command prompt, type
+
+    'python setup.py install' 
+    
+# Running tests
+
+The tests directory contains scripts for testing the computation of 
+the likelihoods, gradients, and maximum likelihood solutions
+To run these tests, a further dependency is required: numdifftools. 
+
+To run the tests, first install sibreg. Change to the tests/ directory and at the shell type
+
+    'python test.py'
+
+Tests should run without any failures.

bin/sGWAS.py

@@ -0,0 +1 @@
+import sibreg

docs/conf.py

@@ -0,0 +1,166 @@
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../regrnd/'))
+print(sys.path)
+
+# -- 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.autosummary',
+    'numpydoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages']
+
+intersphinx_mapping = {'numpy': ('http://docs.scipy.org/doc/numpy/', None)}
+
+# 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'
+
+# General information about the project.
+project = u'regrnd'
+copyright = u'2017, Alexander Thomas Ian Strudwick Young'
+author = u'Alexander Thomas Ian Strudwick Young'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = u'1.2.0a1'
+# The full version, including alpha/beta/rc tags.
+release = u'1.2.0a1'
+
+# 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 patterns also effect to 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'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- 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 = 'alabaster'
+
+# 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.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'hlmmdoc'
+
+
+# -- 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, 'hlmm.tex', u'hlmm Documentation',
+     u'Alexander Thomas Ian Strudwick Young', '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, 'hlmm', u'hlmm 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, 'hlmm', u'hlmm Documentation',
+     author, 'hlmm', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}

docs/guide.rst

@@ -0,0 +1,42 @@
+Guide
+************
+
+**Introduction**
+
+regrnd is a python library for fitting L2 regularised regression models with repeated observations from the same sample.
+regrnd should be run with Anaconda built with Python 2.7.
+
+A regrnd model (:class:`regrnd.model`) consists of a linear model for the mean along
+with a vector of sample labels that allows for repeated observations from the same sample.
+
+The documentation for the regrnd module (:doc:`regrnd`) contains information on how to define a :class:`regrnd.model`,
+how to optimise a :class:`regrnd.model` given a L2 regularisation parameter, how to predict from
+a :class:`regrnd.model`, and how to simulate a :class:`regrnd.model`.
+
+**Running tests**
+
+To check that the code is working properly and computing likelihoods and gradients accurately, you can
+run tests. In the regrnd/ subdirectory, type
+
+    ``python tests.py``
+
+The output should say
+
+    ``Ran 4 tests in...``
+
+    ``OK``
+
+**Running the code**
+
+In the regrnd/ subdirectory, there is a script 'met_analysis.py'. The script takes one
+command line argument that is the location of the training_data.csv file. Unless you wish to install
+regrnd as a package, the 'met_analysis.py' script should be run from the regrnd/ subdirectory
+so that it can import the code in regrnd/regrnd.py.
+
+The cross-validation code is contained in this script, but it is commmented out as it
+takes some time to run for all the investigated regularisation parameters.
+
+Without modifying the script, it trains the model on the training data using the
+regularisation parameters found by cross-validation. It then predicts
+the 'mets' of the test set, and prints the mean squared error on the test set.
+

docs/index.rst

@@ -0,0 +1,16 @@
+Welcome to regrnd's documentation!
+================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   guide
+   regrnd
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/regrnd.rst

@@ -0,0 +1,11 @@
+Documentation for 'regrnd' module
+=================================
+
+Documentation for the regrnd model class.
+
+.. automodule:: regrnd
+
+.. autoclass:: regrnd.model
+    :members:
+
+.. autofunction:: regrnd.simulate

setup.cfg

@@ -0,0 +1,2 @@
+[metadata]
+description-file = README.md

setup.py

@@ -0,0 +1,40 @@
+from setuptools import setup
+
+setup(name='sibreg',
+      version='1.2.0a1',
+      description='Functions for performing robust GWAS using sibpairs in a random effects model',
+      url='https://github.com/alexTISYoung/sibreg',
+      download_url='https://github.com/AlexTISYoung/hlmm/archive/1.2.0a1.tar.gz',
+      author='Alexander I. Young',
+      author_email='[email protected]',
+      license='MIT',
+      scripts=['bin/sGWAS.py'],
+      classifiers=[
+            # How mature is this project? Common values are
+            #   3 - Alpha
+            #   4 - Beta
+            #   5 - Production/Stable
+            'Development Status :: 3 - Alpha',
+
+            # Indicate who your project is intended for
+            'Intended Audience :: Science/Research',
+            'Topic :: Scientific/Engineering :: Bio-Informatics',
+
+            # Pick your license as you wish (should match "license" above)
+            'License :: OSI Approved :: MIT License',
+
+            # Specify the Python versions you support here. In particular, ensure
+            # that you indicate whether you support Python 2, Python 3 or both.
+            'Programming Language :: Python :: 2.7',
+      ],
+      keywords='statistics genetics',
+      packages=['sibreg'],
+      install_requires=[
+            'numpy',
+            'scipy',
+            'pysnptools'
+        ],
+      extras_require={
+            'test': ['numdifftools'],
+      },
+      zip_safe=False)

sibreg/__init__.py

@@ -0,0 +1 @@
+import sibreg