added docs

.gitignore

@@ -13,5 +13,7 @@ python/target/
 .DS_Store
 __pycache__
 
+# docs
+docs/_build/*
 
 *deepsea_train*

README.md

@@ -2,7 +2,7 @@
 
 Full pipeline for learning TFBS from epigenetic datasets.
 
-![Epitome Diagram](figures/epitome_diagram.png)
+![Epitome Diagram](docs/figures/epitome_diagram.png)
 
 Epitome leverages chromatin accessibility data to predict transcription factor binding sites on a novel cell type of interest. Epitome computes the chromatin similarity between 11 cell types in ENCODE and the novel cell types, and uses chromatin similarity to transfer binding information in known cell types to a novel cell type of interest. 
 
@@ -40,9 +40,7 @@ from epitome.models import *
 radii = [1,3,10,30]
 model = MLP(4, [100, 100, 100, 50], 
             tf.tanh, 
-            train_data, 
-            valid_data, 
-            test_data, 
+            data
             test_celltypes,
             gen_from_peaks, 
             matrix,

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = epitome
+SOURCEDIR     = .
+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)

docs/conf.py

@@ -0,0 +1,157 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# epitome documentation build configuration file, created by
+# sphinx-quickstart on Fri Jun 14 12:50:58 2019.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# 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('.'))
+import sphinx_rtd_theme
+
+# -- 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']
+
+# 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 = 'epitome'
+copyright = '2019, Alyssa Morrow'
+author = 'Alyssa Morrow'
+
+# 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 = '0.0.1'
+# The full version, including alpha/beta/rc tags.
+release = '0.0.1'
+
+# 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 = 'sphinx_rtd_theme'
+
+# 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']
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'epitomedoc'
+
+
+# -- 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, 'epitome.tex', 'epitome Documentation',
+     'Alyssa Morrow', '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, 'epitome', 'epitome 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, 'epitome', 'epitome Documentation',
+     author, 'epitome', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+

docs/index.rst

@@ -0,0 +1,31 @@
+.. epitome documentation master file, created by
+
+Introduction
+============
+
+Epitome is a computation model that leverages chromatin accessibility data to predict transcription factor binding sites on a novel cell type of interest. Epitome computes the chromatin similarity between 11 cell types in ENCODE and the novel cell types, and uses chromatin similarity to transfer binding information in known cell types to a novel cell type of interest.
+
+.. image:: figures/epitome_diagram.png
+
+
+.. toctree::
+   :caption: Installation
+   :maxdepth: 2
+
+   installation/source
+
+.. toctree::
+   :caption: Usage and Examples
+   :maxdepth: 2
+
+   usage/train
+   usage/predict
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/installation/source.rst

@@ -0,0 +1,48 @@
+Building Epitome from Source
+============================
+
+**Note**: Epitome is configured for tensorflow 1.12/Cuda 9. If you have a different
+version of cuda, update tensorflow-gpu version accordingly.
+
+Requirements
+------------
+
+* `conda <https://docs.conda.io/en/latest/miniconda.html>`__
+* python 3.6
+
+Installation
+------------
+
+1. Create and activate a pytion 3.6 conda venv:
+
+.. code:: bash
+
+	conda create --name EpitomeEnv python=3.6
+	source activate EpitomeEnv
+
+
+2. Get Epitome code:
+
+.. code:: bash
+
+	git clone [email protected]:akmorrow13/epitome.git
+	cd epitome
+
+
+3. Install Epitome and its requirements
+
+.. code:: bash
+
+	pip install -e .
+
+
+
+Configuring Data
+----------------
+
+To download and format training data, run ```bin/get_deepsea_data.py```:
+
+.. code:: bash
+
+	python bin/get_deepsea_data.py 
+	usage: get_deepsea_data.py [-h] --output_path OUTPUT_PATH

docs/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+set SPHINXPROJ=epitome
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/usage/predict.rst

@@ -0,0 +1,6 @@
+Predicting binding from Chromatin Accessibility
+===============================================
+
+To predict on your own data, you need a bed file of peaks called from DNase-seq or ATAC-seq data.
+
+TODO