From 37586ce4a05b74c6a446128d939c88f55756b53e Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Wed, 28 Apr 2021 19:53:32 +0200
Subject: [PATCH] doc/: add doc
---
doc/Makefile | 20 +++++
doc/make.bat | 35 +++++++++
doc/source/README.rst | 152 +++++++++++++++++++++++++++++++++++++
doc/source/bed_handler.rst | 85 +++++++++++++++++++++
doc/source/conf.py | 61 +++++++++++++++
doc/source/gc_content.rst | 45 +++++++++++
doc/source/index.rst | 23 ++++++
doc/source/modules.rst | 9 +++
doc/source/visu.rst | 29 +++++++
9 files changed, 459 insertions(+)
create mode 100644 doc/Makefile
create mode 100644 doc/make.bat
create mode 100644 doc/source/README.rst
create mode 100644 doc/source/bed_handler.rst
create mode 100644 doc/source/conf.py
create mode 100644 doc/source/gc_content.rst
create mode 100644 doc/source/index.rst
create mode 100644 doc/source/modules.rst
create mode 100644 doc/source/visu.rst
diff --git a/doc/Makefile b/doc/Makefile
new file mode 100644
index 0000000..d0c3cbf
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?=
+SPHINXBUILD ?= sphinx-build
+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/doc/make.bat b/doc/make.bat
new file mode 100644
index 0000000..6247f7e
--- /dev/null
+++ b/doc/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+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% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/doc/source/README.rst b/doc/source/README.rst
new file mode 100644
index 0000000..8f8cb64
--- /dev/null
+++ b/doc/source/README.rst
@@ -0,0 +1,152 @@
+BigWig visu
+===========
+
+Description
+-----------
+
+This project contains three mains submodules that can be found in the ``src/`` directory:
+* The module ``bed_handler`` allows to make some operations on bed files. This module was designed for a particular project and it is unlikly that you want to use it.
+* The module ``gc_content`` allows to create violin plots displaying the GC content of the two or more bed files given in input. It also make a Wilcoxon test to see if the regions contains in those bed files show a difference in their GC-content.
+* The module ``visu`` allows to display the coverage from bigwig files, created from different conditions, in specific genomic regions defines in two or more bed files.
+
+Prerequisites
+-------------
+
+This project requires ``python>=3.8`` to work correctly and the following modules must be installed:
+* Lazyparser>=0.2.0
+* Pandas>=1.0.3
+* Loguru>=0.5.3
+* numpy>=1.17.4
+* pyfaidx>=0.5.7
+* biopython>=1.75
+* seaborn>=0.10.1
+* matplotlib>=3.1.2
+
+Usage
+-----
+
+``gc_content`` module
+~~~~~~~~~~~~~~~~~~~~~
+
+To launch the ``gc_content`` module you must enter the following command at the root of this project:
+
+.. code:: console
+
+ $ python3 -m src.gc_content [PARAMS]
+
+
+Where [PARAMS] corresponds to the parameters given to the program. The list of available params is defined below
+
++---------------------+---------------------------------------------------------------------------------------+
+| Required parameters | Description |
++---------------------+---------------------------------------------------------------------------------------+
+| -B / --beds | A list of beds files containing the regions for which we want to display the coverage |
++---------------------+---------------------------------------------------------------------------------------+
+| -b / --bed_names | A list of names identifying each bed files given in the -B / --beds parameter |
++---------------------+---------------------------------------------------------------------------------------+
+| -g / --genome | A Fasta file containing the entire genome of an organism of interest |
++---------------------+---------------------------------------------------------------------------------------+
+
++---------------------+----------------------------------------------------------------------------------------------------+
+| Optional parameters | Description |
++---------------------+----------------------------------------------------------------------------------------------------+
+| -e / --environment | Number of nucleotides to display around the genomic intervals defined in the bed files (default 0) |
++---------------------+----------------------------------------------------------------------------------------------------+
+| -f / --ft_names | A name identifying the kind of genomic intervals defined in the bed files (default: interval) |
++---------------------+----------------------------------------------------------------------------------------------------+
+
+
+Note that you can also display the help for this module by typing:
+
+.. code:: console
+
+ $ python3 -m src.gc_content --help
+
+
+The list of element must be separated by a comma when you're writing the command. For example, for the parameter ``-B`` if you want to enter 3 beds file you can type
+
+.. code:: console
+
+ $ python3 -m src.gc_content -B bed1.bed bed2.bed bed3.bed [...]
+
+
+The ``[...]`` represent the last part of the command to write.
+
+``visu`` module
+~~~~~~~~~~~~~~~
+
+
+To launch the ``visu`` module you must enter the following command at the root of this project:
+
+.. code:: console
+
+ $ python3 -m src.visu [PARAMS]
+
+
+Where [PARAMS] corresponds to the parameters given to the program. The list of available params is defined below
+
++-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Required parameters | Description |
++-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``-d / --design`` | A tabulated file containing 3 columns. The first column contains a bigwig filename, the second contains the condition name and the last one contains the replicate of the condition. |
++-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``-B / --bw_folder`` | The folder containing the bigwig files mentioned in the first column of the 'design' table |
++-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``-r / --region_beds`` | A list of one or many bed files containing the genomic intervals to display |
++-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| -R / --region_names | A list of names identifying genomic intervals insides the beds given with the ``-r / --region_beds`` parameter. |
++-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+
+Example of the content in the design file:
+
++--------+-----------+-----------+
+| bigwig | condition | replicate |
++--------+-----------+-----------+
+| bw1.bw | Cond1 | R1 |
++--------+-----------+-----------+
+| bw2.bw | Cond1 | R2 |
++--------+-----------+-----------+
+| bw1.bw | Cond2 | R1 |
++--------+-----------+-----------+
+| bw2.bw | Cond2 | R2 |
++--------+-----------+-----------+
+
+
+
++------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Optional parameters | Description |
++------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| -n / --nb_bin | An integer corresponding to the number of bins to use to represent the genomic intervals given with -r / --region_beds arguments. (default 100) |
++------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| -f / --figure_type | The kind of representation wanted (barplot or metagene) (default metagene) |
++------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| -N / --norm | A number corresponding to a bin for which the coverage will become 1. 'None' for no normalisation (default 'None'). Note that this parameter can also take a file (description after this table) |
++------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| -s / --show_replicates | 'y' to create a figure showing the coverage for all replicates 'n' to display only the average coverage across the conditions defined in -d / --design parameter. (default y) |
++------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| -e / --environment | A list of two integers. The first corresponds to the number of nucleotides to display around the genomic intervals of interest defined with the -r / --region_beds parameter and the second corresponds to the number of bins to use (default 0 0) |
++------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| -b / --border_name | A list of two strings. The name of the left and right border to display in the figures between the genomic intervals defined with the -r / --region_beds and their environment (default '' '') |
++------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| -o / --output | Folder where the figures will be stored (default .) |
++------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| -y / --ylim | A list of two integers that corresponds to the y-axis range in the figure. (default None) |
++------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+
+The figure to give to the ``--norm`` parameter must be defined like this:
+
++-----------+----------+-----------+------+
+| condition | region | replicate | coef |
++-----------+----------+-----------+------+
+| Cond1 | interval | R1 | 0.5 |
++-----------+----------+-----------+------+
+| Cond1 | interval | R2 | 0.4 |
++-----------+----------+-----------+------+
+| Cond2 | interval | R1 | 0.84 |
++-----------+----------+-----------+------+
+| Cond2 | interval | R2 | 0.2 |
++-----------+----------+-----------+------+
+
+* The column condition must contain the same conditions defined in the ``condition`` column of the design file.
+* The column replicate must contain the same replicates names in the ``replicate`` column of the design file.
+* The column coef contain a value used to normalise the coverage
diff --git a/doc/source/bed_handler.rst b/doc/source/bed_handler.rst
new file mode 100644
index 0000000..d93013a
--- /dev/null
+++ b/doc/source/bed_handler.rst
@@ -0,0 +1,85 @@
+bed\_handler package
+====================
+
+Submodules
+----------
+
+bed\_handler.bed\_resize module
+-------------------------------
+
+.. automodule:: src.bed_handler.bed_resize
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bed\_handler.config module
+--------------------------
+
+.. automodule:: src.bed_handler.config
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bed\_handler.filter\_bed module
+-------------------------------
+
+.. automodule:: src.bed_handler.filter_bed
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bed\_handler.filter\_gene module
+--------------------------------
+
+.. automodule:: src.bed_handler.filter_gene
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bed\_handler.get\_gene\_locations module
+----------------------------------------
+
+.. automodule:: src.bed_handler.get_gene_locations
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bed\_handler.get\_gene\_regulated\_by\_ddx module
+-------------------------------------------------
+
+.. automodule:: src.bed_handler.get_gene_regulated_by_ddx
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bed\_handler.get\_last\_exons module
+------------------------------------
+
+.. automodule:: src.bed_handler.get_last_exons
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bed\_handler.get\_other\_exon\_in\_same\_gene module
+----------------------------------------------------
+
+.. automodule:: src.bed_handler.get_other_exon_in_same_gene
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bed\_handler.select\_regulated\_near\_ctcf\_exons module
+--------------------------------------------------------
+
+.. automodule:: src.bed_handler.select_regulated_near_ctcf_exons
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: src.bed_handler
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/source/conf.py b/doc/source/conf.py
new file mode 100644
index 0000000..9fc21bf
--- /dev/null
+++ b/doc/source/conf.py
@@ -0,0 +1,61 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- 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('.'))
+#sys.path.insert(0, os.path.abspath('../'))
+#sys.path.insert(0, os.path.abspath('../../'))
+sys.path.insert(0, os.path.abspath('../../'))
+#sys.path.insert(0, os.path.abspath('../../src/bed_handler'))
+#sys.path.insert(0, os.path.abspath('../../src/gc_content'))
+#sys.path.insert(0, os.path.abspath('../../src/visu'))
+
+# -- Project information -----------------------------------------------------
+
+project = 'bigwig_visu'
+copyright = '2021, Fontrodona'
+author = 'Fontrodona'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# 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']
+
+# 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 = []
+
+
+# -- 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'
+
+# 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']
diff --git a/doc/source/gc_content.rst b/doc/source/gc_content.rst
new file mode 100644
index 0000000..30ce374
--- /dev/null
+++ b/doc/source/gc_content.rst
@@ -0,0 +1,45 @@
+gc\_content package
+===================
+
+Submodules
+----------
+
+gc\_content.config module
+-------------------------
+
+.. automodule:: src.gc_content.config
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+gc\_content.gc\_content module
+------------------------------
+
+.. automodule:: src.gc_content.gc_content
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+gc\_content.gc\_stats module
+----------------------------
+
+.. automodule:: src.gc_content.gc_stats
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+gc\_content.stat\_annot module
+------------------------------
+
+.. automodule:: src.gc_content.stat_annot
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: src.gc_content
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/source/index.rst b/doc/source/index.rst
new file mode 100644
index 0000000..7c0009c
--- /dev/null
+++ b/doc/source/index.rst
@@ -0,0 +1,23 @@
+.. bigwig_visu documentation master file, created by
+ sphinx-quickstart on Wed Apr 28 18:56:52 2021.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to bigwig_visu's documentation!
+=======================================
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+
+ README.rst
+ modules.rst
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/doc/source/modules.rst b/doc/source/modules.rst
new file mode 100644
index 0000000..5d3a00d
--- /dev/null
+++ b/doc/source/modules.rst
@@ -0,0 +1,9 @@
+src
+===
+
+.. toctree::
+ :maxdepth: 4
+
+ bed_handler
+ gc_content
+ visu
diff --git a/doc/source/visu.rst b/doc/source/visu.rst
new file mode 100644
index 0000000..f9c2ba3
--- /dev/null
+++ b/doc/source/visu.rst
@@ -0,0 +1,29 @@
+visu package
+============
+
+Submodules
+----------
+
+visu.config module
+------------------
+
+.. automodule:: src.visu.config
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+visu.figure\_maker module
+-------------------------
+
+.. automodule:: src.visu.figure_maker
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: src.visu
+ :members:
+ :undoc-members:
+ :show-inheritance:
--
GitLab