Mercurial > repos > vimalkumarvelayudhan > riboplot
changeset 18:cff63cf0dea8
Update tool_dependencies to install package from pip
| author | Vimalkumar Velayudhan <vimal@biotechcoder.com> |
|---|---|
| date | Mon, 31 Aug 2015 14:13:03 +0100 |
| parents | 805b779d4013 |
| children | a013fc01d8f3 |
| files | AUTHORS.rst CONTRIBUTING.rst HISTORY.rst LICENSE MANIFEST.in Makefile README.rst docs/Makefile docs/_static/alabaster.css_t docs/_static/riboplot-logo.png docs/_styles/custom.style docs/_styles/fonts/Cabin-Bold.ttf docs/_styles/fonts/Cabin-BoldItalic.ttf docs/_styles/fonts/Cabin-Italic.ttf docs/_styles/fonts/Cabin-Regular.ttf docs/_styles/fonts/SourceSansPro-Bold.ttf docs/_styles/fonts/SourceSansPro-BoldItalic.ttf docs/_styles/fonts/SourceSansPro-Italic.ttf docs/_styles/fonts/SourceSansPro-Regular.ttf docs/_templates/about.html docs/_templates/layout.html docs/_templates/searchbox.html docs/authors.rst docs/conf.py docs/contributing.rst docs/history.rst docs/index.rst docs/installation.rst docs/make.bat docs/readme.rst docs/todo.rst docs/usage.rst images/ribocount.png images/riboplot.png ribocount.xml riboplot.egg-info/PKG-INFO riboplot.egg-info/SOURCES.txt riboplot.egg-info/dependency_links.txt riboplot.egg-info/entry_points.txt riboplot.egg-info/not-zip-safe riboplot.egg-info/requires.txt riboplot.egg-info/top_level.txt riboplot.xml riboplot/__init__.py riboplot/config.py riboplot/data/css/asc.gif riboplot/data/css/bg.gif riboplot/data/css/custom.css riboplot/data/css/desc.gif riboplot/data/css/normalize.css riboplot/data/css/skeleton.css riboplot/data/js/custom.js riboplot/data/js/jquery-1.11.3.min.js riboplot/data/js/jquery-1.11.3.min.map riboplot/data/js/jquery.tablesorter.min.js riboplot/data/ribocount.html riboplot/data/ribocount_index.html riboplot/data/riboplot.html riboplot/ribocore.py riboplot/ribocount.py riboplot/riboplot.py riboplot/scripts/run_coverage.sh riboplot/scripts/run_ribocount_sample.sh riboplot/scripts/run_riboplot_sample.sh riboplot/scripts/run_tests.sh setup.cfg setup.py tests/README.rst tests/__init__.py tests/data/css tests/data/js tests/data/ribocount.html tests/data/ribocount_index.html tests/data/riboplot.html tests/test_ribocount.py tests/test_riboplot.py tool_dependencies.xml tox.ini |
| diffstat | 77 files changed, 58 insertions(+), 4182 deletions(-) [+] |
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--- a/AUTHORS.rst Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -======= -Credits -======= - -Development Lead ----------------- - -* Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> - -Contributors ------------- - -None yet. Why not be the first? \ No newline at end of file
--- a/CONTRIBUTING.rst Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,111 +0,0 @@ -============ -Contributing -============ - -Contributions are welcome, and they are greatly appreciated! Every -little bit helps, and credit will always be given. - -You can contribute in many ways: - -Types of Contributions ----------------------- - -Report Bugs -~~~~~~~~~~~ - -Report bugs at https://github.com/vimalkumarvelayudhan/riboplot/issues. - -If you are reporting a bug, please include: - -* Your operating system name and version. -* Any details about your local setup that might be helpful in troubleshooting. -* Detailed steps to reproduce the bug. - -Fix Bugs -~~~~~~~~ - -Look through the GitHub issues for bugs. Anything tagged with "bug" -is open to whoever wants to implement it. - -Implement Features -~~~~~~~~~~~~~~~~~~ - -Look through the GitHub issues for features. Anything tagged with "feature" -is open to whoever wants to implement it. - -Write Documentation -~~~~~~~~~~~~~~~~~~~ - -RiboPlot could always use more documentation, whether as part of the -official RiboPlot docs, in docstrings, or even on the web in blog posts, -articles, and such. - -Submit Feedback -~~~~~~~~~~~~~~~ - -The best way to send feedback is to file an issue at https://github.com/vimalkumarvelayudhan/riboplot/issues. - -If you are proposing a feature: - -* Explain in detail how it would work. -* Keep the scope as narrow as possible, to make it easier to implement. -* Remember that this is a volunteer-driven project, and that contributions - are welcome :) - -Get Started! ------------- - -Ready to contribute? Here's how to set up `riboplot` for local development. - -1. Fork the `riboplot` repo on GitHub. -2. Clone your fork locally:: - - $ git clone git@github.com:your_name_here/riboplot.git - -3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:: - - $ mkvirtualenv riboplot - $ cd riboplot/ - $ python setup.py develop - -4. Create a branch for local development:: - - $ git checkout -b name-of-your-bugfix-or-feature - - Now you can make your changes locally. - -5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox:: - - $ flake8 riboplot tests - $ python setup.py test - $ tox - - To get flake8 and tox, just pip install them into your virtualenv. - -6. Commit your changes and push your branch to GitHub:: - - $ git add . - $ git commit -m "Your detailed description of your changes." - $ git push origin name-of-your-bugfix-or-feature - -7. Submit a pull request through the GitHub website. - -Pull Request Guidelines ------------------------ - -Before you submit a pull request, check that it meets these guidelines: - -1. The pull request should include tests. -2. If the pull request adds functionality, the docs should be updated. Put - your new functionality into a function with a docstring, and add the - feature to the list in README.rst. -3. The pull request should work for Python 2.6, 2.7, 3.3, and 3.4, and for PyPy. Check - https://travis-ci.org/vimalkumarvelayudhan/riboplot/pull_requests - and make sure that the tests pass for all supported Python versions. - -Tips ----- - -To run a subset of tests:: - - $ python -m unittest tests.test_riboplot \ No newline at end of file
--- a/HISTORY.rst Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -.. :changelog: - -History -======= - -0.1.0 (2015-08-24) ---------------------- - -* First release on PyPI.
--- a/LICENSE Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -Copyright (c) 2015, Vimalkumar Velayudhan -All rights reserved. - -Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: - -* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. - -* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. - -* Neither the name of RiboPlot nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. \ No newline at end of file
--- a/MANIFEST.in Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -recursive-exclude * *.py[co] -exclude riboplot/riboplot_multi.py
--- a/Makefile Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,69 +0,0 @@ -.PHONY: clean-pyc clean-build docs clean - -help: - @echo "clean - remove all build, test, coverage and Python artifacts" - @echo "clean-build - remove build artifacts" - @echo "clean-pyc - remove Python file artifacts" - @echo "clean-test - remove test and coverage artifacts" - @echo "lint - check style with flake8" - @echo "test - run tests quickly with the default Python" - @echo "test-all - run tests on every Python version with tox" - @echo "coverage - check code coverage quickly with the default Python" - @echo "docs - generate Sphinx HTML documentation, including API docs" - @echo "release - package and upload a release" - @echo "dist - package" - @echo "install - install the package to the active Python's site-packages" - -clean: clean-build clean-pyc clean-test - -clean-build: - rm -fr build/ - rm -fr dist/ - rm -fr .eggs/ - find . -name '*.egg-info' -exec rm -fr {} + - find . -name '*.egg' -exec rm -f {} + - -clean-pyc: - find . -name '*.pyc' -exec rm -f {} + - find . -name '*.pyo' -exec rm -f {} + - find . -name '*~' -exec rm -f {} + - find . -name '__pycache__' -exec rm -fr {} + - -clean-test: - rm -fr .tox/ - rm -f .coverage - rm -fr htmlcov/ - -lint: - flake8 riboplot tests - -test: - python setup.py test - -test-all: - tox - -coverage: - coverage run --source riboplot setup.py test - coverage report -m - coverage html - open htmlcov/index.html - -docs: - rm -f docs/riboplot.rst - rm -f docs/modules.rst - sphinx-apidoc -o docs/ riboplot - $(MAKE) -C docs clean - $(MAKE) -C docs html - -release: clean - python setup.py sdist upload - python setup.py bdist_wheel upload - -dist: clean - python setup.py sdist - python setup.py bdist_wheel - ls -l dist - -install: clean - python setup.py install
--- a/README.rst Mon Aug 31 11:41:48 2015 +0100 +++ b/README.rst Mon Aug 31 14:13:03 2015 +0100 @@ -1,6 +1,6 @@ -=============================== +======== RiboPlot -=============================== +======== .. image:: https://img.shields.io/travis/vimalkumarvelayudhan/riboplot.svg :target: https://travis-ci.org/vimalkumarvelayudhan/riboplot @@ -14,13 +14,39 @@ There are two programs in the package: **riboplot** + Plot and output read counts (csv) for a single transcript. **ribocount** + Output read counts for all transcripts in an alignment. +Free software: GPL license -Free software: GPL license. +Documentation: https://riboplot.readthedocs.org + +Repository: https://github.com/vimalkumarvelayudhan/riboplot + +Requirements +------------ +Python packages +............... +* matplotlib ``1.3.1`` +* pysam ``0.8.3`` -Documentation: https://riboplot.readthedocs.org. +If you have a virtualenv setup, these packages and their dependencies can be installed +using:: + + pip install matplotlib==1.3.1 + pip install pysam==0.8.3 +Bedtools +........ +RNA coverage plot requires `bedtools <https://github.com/arq5x/bedtools2>`_ to be installed. + +This release of riboplot has been tested with bedtools version ``2.17.0``. + +On Ubuntu and derivatives, bedtools can be installed from the repositories using:: + + sudo apt-get install bedtools +
--- a/docs/Makefile Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,177 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -PAPER = -BUILDDIR = _build - -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) -$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) -endif - -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . -# the i18n builder cannot share the environment and doctrees with the others -I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . - -.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext - -help: - @echo "Please use \`make <target>' where <target> is one of" - @echo " html to make standalone HTML files" - @echo " dirhtml to make HTML files named index.html in directories" - @echo " singlehtml to make a single large HTML file" - @echo " pickle to make pickle files" - @echo " json to make JSON files" - @echo " htmlhelp to make HTML files and a HTML help project" - @echo " qthelp to make HTML files and a qthelp project" - @echo " devhelp to make HTML files and a Devhelp project" - @echo " epub to make an epub" - @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" - @echo " latexpdf to make LaTeX files and run them through pdflatex" - @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" - @echo " text to make text files" - @echo " man to make manual pages" - @echo " texinfo to make Texinfo files" - @echo " info to make Texinfo files and run them through makeinfo" - @echo " gettext to make PO message catalogs" - @echo " changes to make an overview of all changed/added/deprecated items" - @echo " xml to make Docutils-native XML files" - @echo " pseudoxml to make pseudoxml-XML files for display purposes" - @echo " linkcheck to check all external links for integrity" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - -clean: - rm -rf $(BUILDDIR)/* - -html: - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." - -dirhtml: - $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." - -singlehtml: - $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml - @echo - @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." - -pickle: - $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle - @echo - @echo "Build finished; now you can process the pickle files." - -json: - $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json - @echo - @echo "Build finished; now you can process the JSON files." - -htmlhelp: - $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp - @echo - @echo "Build finished; now you can run HTML Help Workshop with the" \ - ".hhp project file in $(BUILDDIR)/htmlhelp." - -qthelp: - $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp - @echo - @echo "Build finished; now you can run "qcollectiongenerator" with the" \ - ".qhcp project file in $(BUILDDIR)/qthelp, like this:" - @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/riboplot.qhcp" - @echo "To view the help file:" - @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/riboplot.qhc" - -devhelp: - $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp - @echo - @echo "Build finished." - @echo "To view the help file:" - @echo "# mkdir -p $$HOME/.local/share/devhelp/riboplot" - @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/riboplot" - @echo "# devhelp" - -epub: - $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub - @echo - @echo "Build finished. The epub file is in $(BUILDDIR)/epub." - -latex: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo - @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." - @echo "Run \`make' in that directory to run these through (pdf)latex" \ - "(use \`make latexpdf' here to do that automatically)." - -latexpdf: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through pdflatex..." - $(MAKE) -C $(BUILDDIR)/latex all-pdf - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -latexpdfja: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through platex and dvipdfmx..." - $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -text: - $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text - @echo - @echo "Build finished. The text files are in $(BUILDDIR)/text." - -man: - $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man - @echo - @echo "Build finished. The manual pages are in $(BUILDDIR)/man." - -texinfo: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo - @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." - @echo "Run \`make' in that directory to run these through makeinfo" \ - "(use \`make info' here to do that automatically)." - -info: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo "Running Texinfo files through makeinfo..." - make -C $(BUILDDIR)/texinfo info - @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." - -gettext: - $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale - @echo - @echo "Build finished. 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--- a/docs/_static/alabaster.css_t Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,612 +0,0 @@ -{% set sidebar_width = '300px' %} - -{% set theme_sidebar_header = theme_sidebar_header or theme_gray_1 %} -{% set theme_sidebar_link = theme_sidebar_link or theme_gray_1 %} -{% set theme_anchor_hover_fg = theme_anchor_hover_fg or theme_gray_1 %} - -{% set theme_note_bg = theme_note_bg or theme_gray_2 %} -{% set theme_footnote_border = theme_footnote_border or theme_gray_2 %} -{% set theme_pre_bg = theme_pre_bg or theme_gray_2 %} - -{% set theme_warn_bg = theme_warn_bg or theme_pink_1 %} -{% set theme_warn_border = theme_warn_border or theme_pink_2 %} - -{% set theme_seealso_bg = theme_seealso_bg or theme_gray_2 %} - -{% set theme_narrow_sidebar_link = theme_narrow_sidebar_link or theme_gray_3 %} -{% set theme_sidebar_hr = theme_sidebar_hr or theme_gray_3 %} - - -@import url("basic.css"); - -/* -- page layout ----------------------------------------------------------- */ - -html { - position: relative; - min-height: 100%; -} - -body { - font-family: {{ theme_font_family }}; - font-weight: 300; - font-size: 18px; - line-height: 1.6; - background-color: #ffffff; - color: #333; - margin: 20px 0px 50px 0px; - padding: 0; -} - -div.document { - margin: 0px 30px; -} - -div.documentwrapper { - float: left; - width: 100%; -} - -div.bodywrapper { - margin: 0 0 0 320px; - padding-left: 1px; - border-left: 1px dotted #f0f0f0; -} - -div.sphinxsidebar { - width: {{ sidebar_width }}; -} - -hr { - border: 1px solid #B1B4B6; -} - -div.body { - background-color: #ffffff; - color: {{ theme_body_text }}; - padding: 0 30px 0 30px; -} - -div.footer { - position: absolute; - bottom: 0; - width: 100%; - height: 50px; - font-size: 0.4em; - color: {{ theme_footer_text }}; - text-align: center; -} - -div.footer a { - color: {{ theme_footer_text }}; -} - -div.related { - display: none; -} - -div.sphinxsidebar a { - color: {{ theme_link }}; - text-decoration: none; - /*border-bottom: 1px dotted {{ theme_sidebar_link_underscore }};*/ -} - -div.sphinxsidebar a:hover { - border-bottom: 1px solid {{ theme_sidebar_link_underscore }}; -} - -div.sphinxsidebar { - font-size: 16px; - line-height: 1.5; -} - -div.sphinxsidebarwrapper { - padding: 18px 10px; -} - -div.sphinxsidebarwrapper p.logo { - padding: 0; - margin: -10px 0 10px 0px; - text-align: left; -} - -div.sphinxsidebarwrapper h1.logo { - margin-top: -10px; - text-align: center; - margin-bottom: 20px; - text-align: {{ theme_logo_text_align }}; - font-family: {{ theme_head_font_family }} -} - -div.sphinxsidebarwrapper h1.logo-name { - margin-top: 0px; -} - -div.sphinxsidebarwrapper p.blurb { - margin-top: 0; - font-style: {{ theme_description_font_style }}; -} - -div.sphinxsidebar h3, -div.sphinxsidebar h4 { - font-family: {{ theme_head_font_family }}; - color: {{ theme_sidebar_header }}; - font-size: 24px; - font-weight: normal; - margin: 0 0 5px 0; - padding: 0; -} - -div.sphinxsidebar h4 { - font-size: 20px; -} - -div.sphinxsidebar h3 a { - color: {{ theme_link }}; -} - -div.sphinxsidebar p.logo a, -div.sphinxsidebar h3 a, -div.sphinxsidebar p.logo a:hover, -div.sphinxsidebar h3 a:hover { - border: none; 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- font-weight: 400; - line-height: 1.4; - margin: 30px 0px 10px 0px; - padding: 0; - color: #666; -} - -div.body h1 { margin-top: 0; padding-top: 0; font-size: 240%; } -div.body h2 { font-size: 180%; } -div.body h3 { font-size: 150%; } -div.body h4 { font-size: 130%; } -div.body h5 { font-size: 100%; } -div.body h6 { font-size: 100%; } - -a.headerlink { - color: {{ theme_anchor }}; - padding: 0 4px; - text-decoration: none; -} - -a.headerlink:hover { - color: {{ theme_anchor_hover_fg }}; - background: {{ theme_anchor_hover_bg }}; -} - -div.admonition { - margin: 20px 0px; - padding: 10px 30px; - background-color: {{ theme_warn_bg }}; - border: 1px solid {{ theme_warn_border }}; -} - -div.admonition tt.xref, div.admonition a tt { - border-bottom: 1px solid #fafafa; -} - -dd div.admonition { - margin-left: -60px; - padding-left: 60px; -} - -div.admonition p.admonition-title { - margin: 0 0 10px 0; - padding: 0; - line-height: 1; -} - -div.admonition p.last { - margin-bottom: 0; -} - -div.highlight { - background-color: white; -} - -dt:target, .highlight { - background: #FAF3E8; -} - -div.note { - background-color: {{ theme_note_bg }}; - border: 1px solid {{ theme_note_border }}; -} - -div.seealso { - background-color: {{ theme_seealso_bg }}; - border: 1px solid {{ theme_seealso_border }}; -} - -div.topic { - background-color: #eee; -} - -p.admonition-title { - display: inline; -} - -p.admonition-title:after { - content: ":"; -} - -em { - color: #313131; -} - -pre, tt, code { - font-family: {{theme_code_font_family}}; - font-size: {{ theme_code_font_size }}; - font-weight: 400; -} - -img.screenshot { -} - -tt.descname, tt.descclassname, code.descname, code.descclassname { - font-size: 0.95em; -} - -tt.descname, code.descname { - padding-right: 0.08em; -} - -img.screenshot { - -moz-box-shadow: 2px 2px 4px #eee; - -webkit-box-shadow: 2px 2px 4px #eee; - box-shadow: 2px 2px 4px #eee; -} - -table.docutils { - border: 1px solid #888; - -moz-box-shadow: 2px 2px 4px #eee; - -webkit-box-shadow: 2px 2px 4px #eee; - box-shadow: 2px 2px 4px #eee; -} - -table.docutils td, table.docutils th { - border: 1px solid #888; - padding: 0.25em 0.7em; -} - -table.field-list, table.footnote { - border: none; - -moz-box-shadow: none; - -webkit-box-shadow: none; - box-shadow: none; -} - -table.footnote { - margin: 15px 0; - width: 100%; - border: 1px solid {{ theme_footnote_border }}; - background: {{ theme_footnote_bg }}; - font-size: 0.9em; -} - -table.footnote + table.footnote { - margin-top: -15px; - border-top: none; -} - -table.field-list th { - padding: 0 0.8em 0 0; -} - -table.field-list td { - padding: 0; -} - -table.footnote td.label { - width: 0px; - padding: 0.3em 0 0.3em 0.5em; -} - -table.footnote td { - padding: 0.3em 0.5em; -} - -dl { - margin: 0; - padding: 0; -} - -dl dd { - margin-left: 30px; -} - -blockquote { - margin: 0 0 0 30px; - padding: 0; -} - -ul, ol { - margin: 10px 0 10px 30px; - padding: 0; -} - -pre { - background: {{ theme_pre_bg }}; - padding: 7px 30px; - margin: 15px 0px; - line-height: 1.3em; -} - -dl pre, blockquote pre, li pre { - margin-left: -60px; - padding-left: 60px; -} - -dl dl pre { - margin-left: -90px; - padding-left: 90px; -} - -tt, code { - background-color: {{ theme_pre_bg }}; - color: #444; - /* padding: 1px 2px; */ -} - -tt.xref, code.xref, a tt { - background-color: #FBFBFB; - border-bottom: 1px solid white; -} - -a.reference { - text-decoration: none; - color: {{ theme_link }} -} - -a.reference:hover { - color: {{ theme_link_hover }}; - border-bottom: 1px solid {{ theme_link_hover }}; -} - -a.footnote-reference { - text-decoration: none; - font-size: 0.7em; - vertical-align: top; - border-bottom: 1px dotted {{ theme_link }}; -} - -a.footnote-reference:hover { - border-bottom: 1px solid {{ theme_link_hover }}; -} - -a:hover tt, a:hover code { - background: #EEE; -} - - -@media screen and (max-width: 870px) { - - div.sphinxsidebar { - display: none; - } - - div.document { - width: 100%; - - } - - div.documentwrapper { - margin-left: 0; - margin-top: 0; - margin-right: 0; - margin-bottom: 0; - } - - div.bodywrapper { - margin-top: 0; - margin-right: 0; - margin-bottom: 0; - margin-left: 0; - border-left: 0px; - } - - ul { - margin-left: 0; - } - - .document { - width: auto; - } - - .footer { - width: auto; - } - - .bodywrapper { - margin: 0; - } - - .footer { - width: auto; - } - - .github { - display: none; - } - - - -} - - - -@media screen and (max-width: 875px) { - - body { - margin: 0; - padding: 20px 30px; - } - - div.documentwrapper { - float: none; - background: white; - } - - div.sphinxsidebar { - display: block; - float: none; - width: 102.5%; - margin: 50px -30px -20px -30px; - padding: 10px 20px; - background: {{ theme_narrow_sidebar_bg }}; - color: {{ theme_narrow_sidebar_fg }}; - } - - div.sphinxsidebar h3, div.sphinxsidebar h4, div.sphinxsidebar p, - div.sphinxsidebar h3 a { - color: white; - } - - div.sphinxsidebar a { - color: {{ theme_narrow_sidebar_link }}; - } - - div.sphinxsidebar p.logo { - display: none; - } - - div.document { - width: 100%; - margin: 0; - } - - div.related { - display: block; - margin: 0; - padding: 10px 0 20px 0; - } - - div.related ul, - div.related ul li { - margin: 0; - padding: 0; - } - - div.footer { - display: none; - } - - div.bodywrapper { - margin: 0; - } - - div.body { - min-height: 0; - padding: 0; - } - - .rtd_doc_footer { - display: none; - } - - .document { - width: auto; - } - - .footer { - width: auto; - } - - .footer { - width: auto; - } - - .github { - display: none; - } -} - - -/* misc. */ - -.revsys-inline { - display: none!important; -} - -/* Make nested-list/multi-paragraph items look better in Releases changelog - * pages. Without this, docutils' magical list fuckery causes inconsistent - * formatting between different release sub-lists. - */ -div#changelog > div.section > ul > li > p:only-child { - margin-bottom: 0; -} - -/* Hide fugly table cell borders in ..bibliography:: directive output */ -table.docutils.citation, table.docutils.citation td, table.docutils.citation th { - border:none; -} - -#searchbox { - margin-top: 1.5em; - margin-bottom: 1.5em; -} - -div.sphinxsidebar #searchbox input[type="text"] { - width: 220px; -} - -div.sphinxsidebar #searchbox input[type="submit"] { - width: 40px; -}
--- a/docs/_styles/custom.style Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ - { - "fontsAlias" : { - "stdFont": "Open Sans :style=Regular", - "stdBold": "Open Sans :style=Bold", - "stdItalic": "Open Sans :style=Italic", - "stdBoldItalic": "Open Sans :style=Bold Italic", - "stdMono": "Source Code Pro", - "stdMonoItalic": "Source Code Pro", - "stdMonoBold": "Source Code Pro", - "stdMonoBoldItalic": "Source Code Pro" - }, - "styles": { - "base": { - "leading": 14 - }, - "literal": { - "backColor": "#fffce6", - "fontSize": 9 - }, - "code": { - "backColor": "#f9f9f9", - "borderColor": "#f1f1f1", - "fontSize": 9 - }, - "admonition": { - "backColor": "#f9f9f9" - }, - "note": { - "backColor": "#e6f7ff", - "borderColor": "#ccefff" - } - } - } \ No newline at end of file
--- a/docs/_templates/about.html Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -<h1 class="logo"><a href="{{ pathto(master_doc) }}">{{ project }}</a></h1>
--- a/docs/_templates/layout.html Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ -{%- extends "basic/layout.html" %} -{%- block extrahead %} - {{ super() }} - {% if theme_touch_icon %} - <link rel="apple-touch-icon" href="{{ pathto('_static/' ~ theme_touch_icon, 1) }}" /> - {% endif %} - <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9"> -{% endblock %} -{%- block relbar2 %}{% endblock %} -{%- block footer %} - <div class="footer"> - <small> - {%- if last_updated %} - {% trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %} - {%- endif %} - </small> - - {% if theme_show_powered_by|lower == 'true' %} - | - Powered by <a href="http://sphinx-doc.org/">Sphinx {{ sphinx_version }}</a> - & <a href="https://github.com/bitprophet/alabaster">Alabaster {{ alabaster_version }}</a> - {% endif %} - {%- if show_source and has_source and sourcename %} - | - <a href="{{ pathto('_sources/' + sourcename, true)|e }}" - rel="nofollow">{{ _('Page source') }}</a></li> - {%- endif %} - </div> - - {% if theme_github_banner|lower != 'false' %} - <a href="https://github.com/{{ theme_github_user }}/{{ theme_github_repo }}" class="github"> - <img style="position: absolute; top: 0; right: 0; border: 0;" src="{{ pathto('_static/' ~ theme_github_banner, 1) if theme_github_banner|lower != 'true' else 'http://s3.amazonaws.com/github/ribbons/forkme_right_darkblue_121621.png' }}" alt="Fork me on GitHub" class="github"/> - </a> - {% endif %} - - {% if theme_analytics_id %} - <script type="text/javascript"> - - var _gaq = _gaq || []; - _gaq.push(['_setAccount', '{{ theme_analytics_id }}']); - _gaq.push(['_setDomainName', 'none']); - _gaq.push(['_setAllowLinker', true]); - _gaq.push(['_trackPageview']); - - (function() { - var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; - ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; - var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); - })(); - - </script> - {% endif %} -{%- endblock %}
--- a/docs/_templates/searchbox.html Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -{# - basic/searchbox.html - ~~~~~~~~~~~~~~~~~~~~ - - Sphinx sidebar template: quick search box. - - :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS. - :license: BSD, see LICENSE for details. -#} -{%- if pagename != "search" and builder != "singlehtml" %} -<div id="searchbox" style="display: none" role="search"> - <!--<h3>{{ _('Search') }}</h3>--> - <form class="search" action="{{ pathto('search') }}" method="get"> - <input type="text" name="q" placeholder="Search"/> - <input type="submit" value="{{ _('Go') }}" /> - <input type="hidden" name="check_keywords" value="yes" /> - <input type="hidden" name="area" value="default" /> - </form> -</div> -<script type="text/javascript">$('#searchbox').show(0);</script> -{%- endif %}
--- a/docs/authors.rst Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -../AUTHORS.rst \ No newline at end of file
--- a/docs/conf.py Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,294 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -# -# riboplot documentation build configuration file, created by -# sphinx-quickstart on Tue Jul 9 22:26:36 2013. -# -# 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. - -import sys -import os -# To get the docs to build on readthedocs.org -from mock import Mock as MagicMock - -class Mock(MagicMock): - @classmethod - def __getattr__(cls, name): - return Mock() - -MOCK_MODULES = ['matplotlib'] -sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES) - - -# 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. -#sys.path.insert(0, os.path.abspath('.')) - -# Get the project root dir, which is the parent dir of this -cwd = os.getcwd() -project_root = os.path.dirname(cwd) - -# Insert the project root dir as the first element in the PYTHONPATH. -# This lets us ensure that the source package is imported, and that its -# version is used. -sys.path.insert(0, project_root) - -import riboplot - -# -- 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.viewcode'] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# The suffix of source filenames. -source_suffix = '.rst' - -# The encoding of source files. -#source_encoding = 'utf-8-sig' - -# The master toctree document. -master_doc = 'index' - -# General information about the project. -project = u'RiboPlot' -copyright = u'2015, Vimalkumar Velayudhan' - -# 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 = riboplot.__version__ -# The full version, including alpha/beta/rc tags. -release = riboplot.__version__ - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -#language = None - -# There are two options for replacing |today|: either, you set today to -# some non-false value, then it is used: -#today = '' -# Else, today_fmt is used as the format for a strftime call. -#today_fmt = '%B %d, %Y' - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -exclude_patterns = ['_build'] - -# The reST default role (used for this markup: `text`) to use for all -# documents. -#default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -#add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -#add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -#show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' - -# A list of ignored prefixes for module index sorting. -#modindex_common_prefix = [] - -# If true, keep warnings as "system message" paragraphs in the built -# documents. -#keep_warnings = 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 = {} -html_theme_options = { - 'font_family': '"Source Sans Pro", Ubuntu, sans-serif', - 'head_font_family': 'Cabin, Ubuntu, sans-serif', - 'code_font_family': '"Source Code Pro", "Ubuntu Mono", monospace', - 'code_font_size': '0.8em', - 'pre_bg': '#f9f9f9', 'note_bg': '#e6f7ff', 'note_border': '#ccefff', - 'sidebar_list': '#777777', 'body_text': '#515151', 'show_powered_by': False} - - -# Add any paths that contain custom themes here, relative to this directory. -#html_theme_path = [] - -# The name for this set of Sphinx documents. If None, it defaults to -# "<project> v<release> documentation". -#html_title = None - -# A shorter title for the navigation bar. Default is the same as -# html_title. -html_short_title = 'RiboPlot' - -# The name of an image file (relative to this directory) to place at the -# top of the sidebar. -html_logo = '_static/riboplot-logo.png' - -# The name of an image file (within the static path) to use as favicon -# of the docs. This file should be a Windows icon file (.ico) being -# 16x16 or 32x32 pixels large. -#html_favicon = None - -# 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'] - -# If not '', a 'Last updated on:' timestamp is inserted at every page -# bottom, using the given strftime format. -html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -#html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -#html_sidebars = {} - -# Additional templates that should be rendered to pages, maps page names -# to template names. -#html_additional_pages = {} - -# If false, no module index is generated. -#html_domain_indices = True - -# If false, no index is generated. -#html_use_index = True - -# If true, the index is split into individual pages for each letter. -#html_split_index = False - -# If true, links to the reST sources are added to the pages. -#html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. -# Default is True. -#html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. -# Default is True. -#html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages -# will contain a <link> tag referring to it. The value of this option -# must be the base URL from which the finished HTML is served. -#html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = None - -# Output file base name for HTML help builder. -htmlhelp_basename = 'riboplotdoc' - - -# -- 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': '', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, author, documentclass -# [howto/manual]). -latex_documents = [ - ('index', 'riboplot.tex', - u'RiboPlot Documentation', - u'Vimalkumar Velayudhan', 'manual'), -] - -# The name of an image file (relative to this directory) to place at -# the top of the title page. -#latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings -# are parts, not chapters. -#latex_use_parts = False - -# If true, show page references after internal links. -#latex_show_pagerefs = False - -# If true, show URL addresses after external links. -#latex_show_urls = False - -# Documents to append as an appendix to all manuals. -#latex_appendices = [] - -# If false, no module index is generated. -#latex_domain_indices = True - - -# -- Options for manual page output ------------------------------------ - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - ('index', 'riboplot', - u'RiboPlot Documentation', - [u'Vimalkumar Velayudhan'], 1) -] - -# If true, show URL addresses after external links. -#man_show_urls = False - - -# -- 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 = [ - ('index', 'riboplot', - u'RiboPlot Documentation', - u'Vimalkumar Velayudhan', - 'riboplot', - 'One line description of project.', - 'Miscellaneous'), -] - -# Documents to append as an appendix to all manuals. -#texinfo_appendices = [] - -# If false, no module index is generated. -#texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' - -# If true, do not generate a @detailmenu in the "Top" node's menu. -#texinfo_no_detailmenu = False
--- a/docs/contributing.rst Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -../CONTRIBUTING.rst \ No newline at end of file
--- a/docs/history.rst Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -../HISTORY.rst \ No newline at end of file
--- a/docs/index.rst Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -.. riboplot documentation master file, created by - sphinx-quickstart on Tue Jul 9 22:26:36 2013. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -RiboPlot documentation -====================== - -Contents: - -.. toctree:: - :maxdepth: 2 - - readme - installation - usage - contributing - todo - authors - history - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search`
--- a/docs/installation.rst Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -============ -Installation -============ -At the command line:: - - $ easy_install riboplot - -Or, if you have virtualenvwrapper installed:: - - $ mkvirtualenv riboplot - $ pip install riboplot - -.. note:: - - RNA coverage plot requires `bedtools <https://github.com/arq5x/bedtools2>`_ to be installed. - - This release of riboplot has been tested with bedtools version ``2.17.0``. - - On Ubuntu and derivatives, bedtools can be installed from the repositories using:: - - sudo apt-get install bedtools
--- a/docs/make.bat Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,242 +0,0 @@ -@ECHO OFF - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set BUILDDIR=_build -set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . -set I18NSPHINXOPTS=%SPHINXOPTS% . -if NOT "%PAPER%" == "" ( - set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% - set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% -) - -if "%1" == "" goto help - -if "%1" == "help" ( - :help - echo.Please use `make ^<target^>` where ^<target^> is one of - echo. html to make standalone HTML files - echo. dirhtml to make HTML files named index.html in directories - echo. singlehtml to make a single large HTML file - echo. pickle to make pickle files - echo. json to make JSON files - echo. htmlhelp to make HTML files and a HTML help project - echo. qthelp to make HTML files and a qthelp project - echo. devhelp to make HTML files and a Devhelp project - echo. epub to make an epub - echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter - echo. text to make text files - echo. man to make manual pages - echo. texinfo to make Texinfo files - echo. gettext to make PO message catalogs - echo. changes to make an overview over all changed/added/deprecated items - echo. xml to make Docutils-native XML files - echo. pseudoxml to make pseudoxml-XML files for display purposes - echo. linkcheck to check all external links for integrity - echo. doctest to run all doctests embedded in the documentation if enabled - goto end -) - -if "%1" == "clean" ( - for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i - del /q /s %BUILDDIR%\* - goto end -) - - -%SPHINXBUILD% 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 -) - -if "%1" == "html" ( - %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/html. - goto end -) - -if "%1" == "dirhtml" ( - %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. - goto end -) - -if "%1" == "singlehtml" ( - %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. 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The XML files are in %BUILDDIR%/xml. - goto end -) - -if "%1" == "pseudoxml" ( - %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml. - goto end -) - -:end \ No newline at end of file
--- a/docs/readme.rst Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -../README.rst \ No newline at end of file
--- a/docs/todo.rst Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -Todo ----- -* No way to check if input BAM is RNA-Seq/Ribo-Seq (plot will still be generated in either case). -* Check if BAM is sorted. - -
--- a/docs/usage.rst Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,180 +0,0 @@ -.. _usage: - -===== -Usage -===== - -RiboPlot --------- -Plot and output Ribo-Seq read counts of a single transcript from an alignment file (sorted BAM). - -Parameters -.......... - -1. Ribo-Seq alignment file (Sorted BAM file) -++++++++++++++++++++++++++++++++++++++++++++ -A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM -file should be sorted. This can be done using one of the following methods. - -1. RiboGalaxy_ -> Sort Data -> Sort BAM dataset. -2. ``samtools sort input.bam inputsorted`` - -2. Transcriptome (FASTA) -++++++++++++++++++++++++ -A FASTA format file with sequences of the transcripts. - -3. Name of the transcript to plot (Text) -++++++++++++++++++++++++++++++++++++++++ -The name of the transcript to plot **should** match the name in the transcriptome (FASTA) -and the Ribo-Seq/RNA-Seq alignment (BAM). - -4. RNA coverage [optional] (Sorted BAM file) -++++++++++++++++++++++++++++++++++++++++++++ -If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage. - -5. Read lengths to consider [Optional] (Integer - 0 or greater) -+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -If this option is provided, only Ribo-Seq data of the given length is considered. - -6. Offset [optional] (Integer - 0 or greater) -+++++++++++++++++++++++++++++++++++++++++++++ -If this option is provided, this offset is added to the read alignment positions. - -Output -...... -1. Plots (PNG and SVG) -++++++++++++++++++++++ -Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue) - -RNA coverage as a gray background (if the RNA coverage option was selected). - -The open reading frame architecture appears below the plot with start (ATG) and stop codons ('TAA', 'TAG', 'TGA') in all 3 frames. - -The color codes are start (white) and stop (dark gray). - -.. image:: ../images/riboplot.png - -2. RiboSeq read counts (CSV) -++++++++++++++++++++++++++++ -In 3 frames for each position in the transcript. - - -Command line -............ -``riboplot`` can also be run on the command line. The usage is :: - - usage: riboplot [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA -t TEXT - [-n RNA_FILE] [-l INTEGER] [-s INTEGER] [-m HTML_FILE] - [-o OUTPUT_PATH] [-d] - - Plot and output read counts for a single transcript - - optional arguments: - -h, --help - show this help message and exit - - -n RNA_FILE, --rna_file RNA_FILE - RNA-Seq alignment file (BAM) - - -l INTEGER, --read_length INTEGER - Read length to consider (default: None) - - -s INTEGER, --read_offset INTEGER - Read offset (default: 0) - - -m HTML_FILE, --html_file HTML_FILE - Output file for results (HTML) - - -o OUTPUT_PATH, --output_path OUTPUT_PATH - Files are saved in this directory - - -d, --debug - Flag. Produce debug output - - required arguments: - -b RIBO_FILE, --ribo_file RIBO_FILE - Ribo-Seq alignment file in BAM format - - -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA - FASTA format file of the transcriptome - - -t TEXT, --transcript_name TEXT - Transcript name - -RiboCount ---------- -Output read counts for all transcripts in an alignment. - -Parameters -.......... -1. Ribo-Seq alignment file (Sorted BAM file) -++++++++++++++++++++++++++++++++++++++++++++ -A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM -file should be sorted. This can be done using one of the following methods. - -1. RiboGalaxy_ -> Sort Data -> Sort BAM dataset. -2. ``samtools sort input.bam inputsorted`` - -2. Transcriptome (FASTA) -++++++++++++++++++++++++ -A FASTA format file with sequences of the transcripts. - -3. Read lengths to consider [optional] (Integer - 0 or greater) -+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -If this option is provided, only Ribo-Seq data of the given length is considered. - -4. Offset [optional] (Integer - 0 or greater) -+++++++++++++++++++++++++++++++++++++++++++++ -If this option is provided, this offset is added to the read alignment positions. - -Output -...... -Read counts for all transcripts in the alignment (ZIP) -++++++++++++++++++++++++++++++++++++++++++++++++++++++ -The output file ``ribocount_output.zip`` should first be uncompressed. This will generate -a folder called ``ribocount_output``. Open ``index.html`` in a web browser to view the results of ribocount. - -Total reads for each transcript will be displayed in a table along with the name of the transcript and a link -to the CSV file containing the read counts in 3 frames for each position in the transcript. - -.. image:: ../images/ribocount.png - -Command line -............ -``ribocount`` can also be run on the command line. The usage is :: - - usage: ribocount [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l INTEGER] - [-s INTEGER] [-m HTML_FILE] [-o OUTPUT_PATH] [-d] - - Output read counts for all transcripts - - optional arguments: - - -h, --help show this help message and exit - - -l INTEGER, --read_length INTEGER - Read length to consider (default: None) - - -s INTEGER, --read_offset INTEGER - Read offset (default: 0) - - -m HTML_FILE, --html_file HTML_FILE - - Output file for results (HTML) - - -o OUTPUT_PATH, --output_path OUTPUT_PATH - Files are saved in this directory - - -d, --debug Flag. Produce debug output - - required arguments: - - -b RIBO_FILE, --ribo_file RIBO_FILE - Ribo-Seq alignment file in BAM format - - -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA - FASTA format file of the transcriptome - -.. links -.. _RiboGalaxy: http://ribogalaxy.ucc.ie -
--- a/ribocount.xml Mon Aug 31 11:41:48 2015 +0100 +++ b/ribocount.xml Mon Aug 31 14:13:03 2015 +0100 @@ -2,12 +2,12 @@ <description>Get read counts for all transcripts in an alignment (BAM) </description> <requirements> - <requirement type="package" version="0.8.3">pysam</requirement> + <requirement type="package" version="0.1.0">riboplot</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> - <command interpreter="python">riboplot/ribocount.py + <command interpreter="python">ribocount --ribo_file "${ribo_file}" --transcriptome_fasta "${transcriptome_fasta}" --read_length "${read_length}"
--- a/riboplot.egg-info/PKG-INFO Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -Metadata-Version: 1.1 -Name: riboplot -Version: 0.1.0 -Summary: Plot read counts of RiboSeq data from BAM format alignment files -Home-page: https://github.com/vimalkumarvelayudhan/riboplot -Author: Vimalkumar Velayudhan -Author-email: vimalkumarvelayudhan@gmail.com -License: GPL -Description: =============================== - RiboPlot - =============================== - - .. image:: https://img.shields.io/travis/vimalkumarvelayudhan/riboplot.svg - :target: https://travis-ci.org/vimalkumarvelayudhan/riboplot - - .. image:: https://img.shields.io/pypi/v/riboplot.svg - :target: https://pypi.python.org/pypi/riboplot - - - RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format). - - There are two programs in the package: - - **riboplot** - Plot and output read counts (csv) for a single transcript. - - **ribocount** - Output read counts for all transcripts in an alignment. - - For help on using these programs, please refer to :ref:`usage`. - - - Free software: GPL license. - - Documentation: https://riboplot.readthedocs.org. - - - - - - History - ======= - - 0.1.0 (2015-08-24) - --------------------- - - * First release on PyPI. - -Keywords: riboplot -Platform: UNKNOWN -Classifier: Development Status :: 2 - Pre-Alpha -Classifier: Intended Audience :: Developers -Classifier: License :: OSI Approved :: BSD License -Classifier: Natural Language :: English -Classifier: Programming Language :: Python :: 2 -Classifier: Programming Language :: Python :: 2.6 -Classifier: Programming Language :: Python :: 2.7
--- a/riboplot.egg-info/SOURCES.txt Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -AUTHORS.rst -CONTRIBUTING.rst -HISTORY.rst -LICENSE -MANIFEST.in -README.rst -setup.cfg -setup.py -docs/Makefile -docs/authors.rst -docs/conf.py -docs/contributing.rst -docs/history.rst -docs/index.rst -docs/installation.rst -docs/make.bat -docs/modules.rst -docs/readme.rst -docs/riboplot.rst -docs/todo.rst -docs/usage.rst -riboplot/__init__.py -riboplot/config.py -riboplot/ribocore.py -riboplot/ribocount.py -riboplot/riboplot.py -riboplot.egg-info/PKG-INFO -riboplot.egg-info/SOURCES.txt -riboplot.egg-info/dependency_links.txt -riboplot.egg-info/entry_points.txt -riboplot.egg-info/not-zip-safe -riboplot.egg-info/requires.txt -riboplot.egg-info/top_level.txt -riboplot/data/css -riboplot/data/js -riboplot/data/ribocount.html -riboplot/data/ribocount_index.html -riboplot/data/riboplot.html -riboplot/data/css/asc.gif -riboplot/data/css/bg.gif -riboplot/data/css/custom.css -riboplot/data/css/desc.gif -riboplot/data/css/normalize.css -riboplot/data/css/skeleton.css -riboplot/data/js/custom.js -riboplot/data/js/jquery-1.11.3.min.js -riboplot/data/js/jquery-1.11.3.min.map -riboplot/data/js/jquery.tablesorter.min.js -riboplot/scripts/run_coverage.sh -riboplot/scripts/run_ribocount_sample.sh -riboplot/scripts/run_riboplot_sample.sh -riboplot/scripts/run_tests.sh -tests/README.rst -tests/__init__.py -tests/test_ribocount.py -tests/test_riboplot.py -tests/.ropeproject/config.py -tests/.ropeproject/globalnames -tests/.ropeproject/history -tests/.ropeproject/objectdb \ No newline at end of file
--- a/riboplot.egg-info/dependency_links.txt Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -
--- a/riboplot.egg-info/entry_points.txt Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -[console_scripts] -riboplot = riboplot.riboplot:run -ribocount = riboplot.ribocount:run -
--- a/riboplot.egg-info/not-zip-safe Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -
--- a/riboplot.egg-info/requires.txt Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -matplotlib==1.3.1 -pysam==0.8.3 \ No newline at end of file
--- a/riboplot.egg-info/top_level.txt Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -riboplot
--- a/riboplot.xml Mon Aug 31 11:41:48 2015 +0100 +++ b/riboplot.xml Mon Aug 31 14:13:03 2015 +0100 @@ -2,13 +2,12 @@ <description>Plot and output read counts for a single transcript in an alignment (BAM) </description> <requirements> - <requirement type="package" version="1.2.1">matplotlib</requirement> - <requirement type="package" version="0.8.3">pysam</requirement> + <requirement type="package" version="0.1.0">riboplot</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> - <command interpreter="python">riboplot/riboplot.py + <command interpreter="python">riboplot --ribo_file "${ribo_file}" --transcriptome_fasta "${transcriptome_fasta}" --transcript_name "${transcript_name}"
--- a/riboplot/__init__.py Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -# -*- coding: utf-8 -*- - -__author__ = 'Vimalkumar Velayudhan' -__email__ = 'vimalkumarvelayudhan@gmail.com' -__version__ = '0.1.0'
--- a/riboplot/config.py Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -# -*- coding: utf-8 -*- -import os - - -class Config(object): - # get the running directory of this file, move one level up to get the - # application directory - APP_DIR = os.path.split(os.path.dirname(os.path.abspath(__file__)))[0] - PKG_DATA_DIR = os.path.join(APP_DIR, 'riboplot', 'data') - - -class TestingConfig(Config): - """Testing configuration""" - TEST_DATA_DIR = os.path.join(Config.APP_DIR, 'tests/data') - - -class ProductionConfig(Config): - """Production configuration""" - # Additional variables can be listed here - pass
--- a/riboplot/data/css/custom.css Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ -.info { - font-weight: normal; -} - -.text-muted { - font-size: 0.6em; - text-align: center; - color: #555555; -} - -#main { - text-align: center; -} - -#page-title { - margin-top: 5%; -} - -/* tables */ -table.tablesorter { - border: 1px solid #eeeeee; -} - -table.tablesorter thead tr .header { - background-image: url(bg.gif); - background-repeat: no-repeat; - background-position: center right; - cursor: pointer; -} - -table.tablesorter thead tr .headerSortUp { - background-image: url(asc.gif); -} - -table.tablesorter thead tr .headerSortDown { - background-image: url(desc.gif); -} - -table.tablesorter thead tr .headerSortDown, table.tablesorter thead tr .headerSortUp { - background-color: #eeeeee; -} - -table.tablesorter tbody { - font-family: monospace; -} - -#overlay { - top: 20px; - left: 50%; - position: absolute; - margin-left: -170px; - width: 250px; - text-align: center; - display: none; - margin-top: -10px; - background: #F6FF00; - color: #515151; - padding: 3px; - border-radius: 5px; - box-shadow: 3px 3px 3px #eeeeee; -} \ No newline at end of file
--- a/riboplot/data/css/normalize.css Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,427 +0,0 @@ -/*! normalize.css v3.0.2 | MIT License | git.io/normalize */ - -/** - * 1. Set default font family to sans-serif. - * 2. Prevent iOS text size adjust after orientation change, without disabling - * user zoom. - */ - -html { - font-family: sans-serif; /* 1 */ - -ms-text-size-adjust: 100%; /* 2 */ - -webkit-text-size-adjust: 100%; /* 2 */ -} - -/** - * Remove default margin. - */ - -body { - margin: 0; -} - -/* HTML5 display definitions - ========================================================================== */ - -/** - * Correct `block` display not defined for any HTML5 element in IE 8/9. - * Correct `block` display not defined for `details` or `summary` in IE 10/11 - * and Firefox. - * Correct `block` display not defined for `main` in IE 11. - */ - -article, -aside, -details, -figcaption, -figure, -footer, -header, -hgroup, -main, -menu, -nav, -section, -summary { - display: block; -} - -/** - * 1. Correct `inline-block` display not defined in IE 8/9. - * 2. Normalize vertical alignment of `progress` in Chrome, Firefox, and Opera. - */ - -audio, -canvas, -progress, -video { - display: inline-block; /* 1 */ - vertical-align: baseline; /* 2 */ -} - -/** - * Prevent modern browsers from displaying `audio` without controls. - * Remove excess height in iOS 5 devices. - */ - -audio:not([controls]) { - display: none; - height: 0; -} - -/** - * Address `[hidden]` styling not present in IE 8/9/10. - * Hide the `template` element in IE 8/9/11, Safari, and Firefox < 22. - */ - -[hidden], -template { - display: none; -} - -/* Links - ========================================================================== */ - -/** - * Remove the gray background color from active links in IE 10. - */ - -a { - background-color: transparent; -} - -/** - * Improve readability when focused and also mouse hovered in all browsers. - */ - -a:active, -a:hover { - outline: 0; -} - -/* Text-level semantics - ========================================================================== */ - -/** - * Address styling not present in IE 8/9/10/11, Safari, and Chrome. - */ - -abbr[title] { - border-bottom: 1px dotted; -} - -/** - * Address style set to `bolder` in Firefox 4+, Safari, and Chrome. - */ - -b, -strong { - font-weight: bold; -} - -/** - * Address styling not present in Safari and Chrome. - */ - -dfn { - font-style: italic; -} - -/** - * Address variable `h1` font-size and margin within `section` and `article` - * contexts in Firefox 4+, Safari, and Chrome. - */ - -h1 { - font-size: 2em; - margin: 0.67em 0; -} - -/** - * Address styling not present in IE 8/9. - */ - -mark { - background: #ff0; - color: #000; -} - -/** - * Address inconsistent and variable font size in all browsers. - */ - -small { - font-size: 80%; -} - -/** - * Prevent `sub` and `sup` affecting `line-height` in all browsers. - */ - -sub, -sup { - font-size: 75%; - line-height: 0; - position: relative; - vertical-align: baseline; -} - -sup { - top: -0.5em; -} - -sub { - bottom: -0.25em; -} - -/* Embedded content - ========================================================================== */ - -/** - * Remove border when inside `a` element in IE 8/9/10. - */ - -img { - border: 0; -} - -/** - * Correct overflow not hidden in IE 9/10/11. - */ - -svg:not(:root) { - overflow: hidden; -} - -/* Grouping content - ========================================================================== */ - -/** - * Address margin not present in IE 8/9 and Safari. - */ - -figure { - margin: 1em 40px; -} - -/** - * Address differences between Firefox and other browsers. - */ - -hr { - -moz-box-sizing: content-box; - box-sizing: content-box; - height: 0; -} - -/** - * Contain overflow in all browsers. - */ - -pre { - overflow: auto; -} - -/** - * Address odd `em`-unit font size rendering in all browsers. - */ - -code, -kbd, -pre, -samp { - font-family: monospace, monospace; - font-size: 1em; -} - -/* Forms - ========================================================================== */ - -/** - * Known limitation: by default, Chrome and Safari on OS X allow very limited - * styling of `select`, unless a `border` property is set. - */ - -/** - * 1. Correct color not being inherited. - * Known issue: affects color of disabled elements. - * 2. Correct font properties not being inherited. - * 3. Address margins set differently in Firefox 4+, Safari, and Chrome. - */ - -button, -input, -optgroup, -select, -textarea { - color: inherit; /* 1 */ - font: inherit; /* 2 */ - margin: 0; /* 3 */ -} - -/** - * Address `overflow` set to `hidden` in IE 8/9/10/11. - */ - -button { - overflow: visible; -} - -/** - * Address inconsistent `text-transform` inheritance for `button` and `select`. - * All other form control elements do not inherit `text-transform` values. - * Correct `button` style inheritance in Firefox, IE 8/9/10/11, and Opera. - * Correct `select` style inheritance in Firefox. - */ - -button, -select { - text-transform: none; -} - -/** - * 1. Avoid the WebKit bug in Android 4.0.* where (2) destroys native `audio` - * and `video` controls. - * 2. Correct inability to style clickable `input` types in iOS. - * 3. Improve usability and consistency of cursor style between image-type - * `input` and others. - */ - -button, -html input[type="button"], /* 1 */ -input[type="reset"], -input[type="submit"] { - -webkit-appearance: button; /* 2 */ - cursor: pointer; /* 3 */ -} - -/** - * Re-set default cursor for disabled elements. - */ - -button[disabled], -html input[disabled] { - cursor: default; -} - -/** - * Remove inner padding and border in Firefox 4+. - */ - -button::-moz-focus-inner, -input::-moz-focus-inner { - border: 0; - padding: 0; -} - -/** - * Address Firefox 4+ setting `line-height` on `input` using `!important` in - * the UA stylesheet. - */ - -input { - line-height: normal; -} - -/** - * It's recommended that you don't attempt to style these elements. - * Firefox's implementation doesn't respect box-sizing, padding, or width. - * - * 1. Address box sizing set to `content-box` in IE 8/9/10. - * 2. Remove excess padding in IE 8/9/10. - */ - -input[type="checkbox"], -input[type="radio"] { - box-sizing: border-box; /* 1 */ - padding: 0; /* 2 */ -} - -/** - * Fix the cursor style for Chrome's increment/decrement buttons. For certain - * `font-size` values of the `input`, it causes the cursor style of the - * decrement button to change from `default` to `text`. - */ - -input[type="number"]::-webkit-inner-spin-button, -input[type="number"]::-webkit-outer-spin-button { - height: auto; -} - -/** - * 1. Address `appearance` set to `searchfield` in Safari and Chrome. - * 2. Address `box-sizing` set to `border-box` in Safari and Chrome - * (include `-moz` to future-proof). - */ - -input[type="search"] { - -webkit-appearance: textfield; /* 1 */ - -moz-box-sizing: content-box; - -webkit-box-sizing: content-box; /* 2 */ - box-sizing: content-box; -} - -/** - * Remove inner padding and search cancel button in Safari and Chrome on OS X. - * Safari (but not Chrome) clips the cancel button when the search input has - * padding (and `textfield` appearance). - */ - -input[type="search"]::-webkit-search-cancel-button, -input[type="search"]::-webkit-search-decoration { - -webkit-appearance: none; -} - -/** - * Define consistent border, margin, and padding. - */ - -fieldset { - border: 1px solid #c0c0c0; - margin: 0 2px; - padding: 0.35em 0.625em 0.75em; -} - -/** - * 1. Correct `color` not being inherited in IE 8/9/10/11. - * 2. Remove padding so people aren't caught out if they zero out fieldsets. - */ - -legend { - border: 0; /* 1 */ - padding: 0; /* 2 */ -} - -/** - * Remove default vertical scrollbar in IE 8/9/10/11. - */ - -textarea { - overflow: auto; -} - -/** - * Don't inherit the `font-weight` (applied by a rule above). - * NOTE: the default cannot safely be changed in Chrome and Safari on OS X. - */ - -optgroup { - font-weight: bold; -} - -/* Tables - ========================================================================== */ - -/** - * Remove most spacing between table cells. - */ - -table { - border-collapse: collapse; - border-spacing: 0; -} - -td, -th { - padding: 0; -} \ No newline at end of file
--- a/riboplot/data/css/skeleton.css Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,419 +0,0 @@ -/* -* Skeleton V2.0.4 -* Copyright 2014, Dave Gamache -* www.getskeleton.com -* Free to use under the MIT license. -* http://www.opensource.org/licenses/mit-license.php -* 12/29/2014 -*/ - - -/* Table of contents -–––––––––––––––––––––––––––––––––––––––––––––––––– -- Grid -- Base Styles -- Typography -- Links -- Buttons -- Forms -- Lists -- Code -- Tables -- Spacing -- Utilities -- Clearing -- Media Queries -*/ - - -/* Grid -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -.container { - position: relative; - width: 100%; - max-width: 960px; - margin: 0 auto; - padding: 0 20px; - box-sizing: border-box; } -.column, -.columns { - width: 100%; - float: left; - box-sizing: border-box; } - -/* For devices larger than 400px */ -@media (min-width: 400px) { - .container { - width: 85%; - padding: 0; } -} - -/* For devices larger than 550px */ -@media (min-width: 550px) { - .container { - width: 80%; } - .column, - .columns { - margin-left: 4%; } - .column:first-child, - .columns:first-child { - margin-left: 0; } - - .one.column, - .one.columns { width: 4.66666666667%; } - .two.columns { width: 13.3333333333%; } - .three.columns { width: 22%; } - .four.columns { width: 30.6666666667%; } - .five.columns { width: 39.3333333333%; } - .six.columns { width: 48%; } - .seven.columns { width: 56.6666666667%; } - .eight.columns { width: 65.3333333333%; } - .nine.columns { width: 74.0%; } - .ten.columns { width: 82.6666666667%; } - .eleven.columns { width: 91.3333333333%; } - .twelve.columns { width: 100%; margin-left: 0; } - - .one-third.column { width: 30.6666666667%; } - .two-thirds.column { width: 65.3333333333%; } - - .one-half.column { width: 48%; } - - /* Offsets */ - .offset-by-one.column, - .offset-by-one.columns { margin-left: 8.66666666667%; } - .offset-by-two.column, - .offset-by-two.columns { margin-left: 17.3333333333%; } - .offset-by-three.column, - .offset-by-three.columns { margin-left: 26%; } - .offset-by-four.column, - .offset-by-four.columns { margin-left: 34.6666666667%; } - .offset-by-five.column, - .offset-by-five.columns { margin-left: 43.3333333333%; } - .offset-by-six.column, - .offset-by-six.columns { margin-left: 52%; } - .offset-by-seven.column, - .offset-by-seven.columns { margin-left: 60.6666666667%; } - .offset-by-eight.column, - .offset-by-eight.columns { margin-left: 69.3333333333%; } - .offset-by-nine.column, - .offset-by-nine.columns { margin-left: 78.0%; } - .offset-by-ten.column, - .offset-by-ten.columns { margin-left: 86.6666666667%; } - .offset-by-eleven.column, - .offset-by-eleven.columns { margin-left: 95.3333333333%; } - - .offset-by-one-third.column, - .offset-by-one-third.columns { margin-left: 34.6666666667%; } - .offset-by-two-thirds.column, - .offset-by-two-thirds.columns { margin-left: 69.3333333333%; } - - .offset-by-one-half.column, - .offset-by-one-half.columns { margin-left: 52%; } - -} - - -/* Base Styles -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -/* NOTE -html is set to 62.5% so that all the REM measurements throughout Skeleton -are based on 10px sizing. So basically 1.5rem = 15px :) */ -html { - font-size: 62.5%; } -body { - font-size: 1.5em; /* currently ems cause chrome bug misinterpreting rems on body element */ - line-height: 1.6; - font-weight: 400; - font-family: "Open Sans", "HelveticaNeue", "Helvetica Neue", Helvetica, Arial, sans-serif; - color: #515151; } - - -/* Typography -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -h1, h2, h3, h4, h5, h6 { - margin-top: 0; - margin-bottom: 2rem; - font-weight: 300; } -h1 { font-size: 4.0rem; line-height: 1.2; letter-spacing: -.1rem;} -h2 { font-size: 3.6rem; line-height: 1.25; letter-spacing: -.1rem; } -h3 { font-size: 3.0rem; line-height: 1.3; letter-spacing: -.1rem; } -h4 { font-size: 2.4rem; line-height: 1.35; letter-spacing: -.08rem; } -h5 { font-size: 1.8rem; line-height: 1.5; letter-spacing: -.05rem; } -h6 { font-size: 1.5rem; line-height: 1.6; letter-spacing: 0; } - -/* Larger than phablet */ -@media (min-width: 550px) { - h1 { font-size: 5.0rem; } - h2 { font-size: 4.2rem; } - h3 { font-size: 3.6rem; } - h4 { font-size: 3.0rem; } - h5 { font-size: 2.4rem; } - h6 { font-size: 1.5rem; } -} - -p { - margin-top: 0; } - - -/* Links -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -a { - color: #00b4ff; } -a:hover { - color: #008CD7; } - - -/* Buttons -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -.button, -button, -input[type="submit"], -input[type="reset"], -input[type="button"] { - display: inline-block; - height: 38px; - padding: 0 30px; - color: #555; - text-align: center; - font-size: 11px; - font-weight: 600; - line-height: 38px; - letter-spacing: .1rem; - text-transform: uppercase; - text-decoration: none; - white-space: nowrap; - background-color: transparent; - border-radius: 4px; - border: 1px solid #bbb; - cursor: pointer; - box-sizing: border-box; } -.button:hover, -button:hover, -input[type="submit"]:hover, -input[type="reset"]:hover, -input[type="button"]:hover, -.button:focus, -button:focus, -input[type="submit"]:focus, -input[type="reset"]:focus, -input[type="button"]:focus { - color: #333; - border-color: #888; - outline: 0; } -.button.button-primary, -button.button-primary, -input[type="submit"].button-primary, -input[type="reset"].button-primary, -input[type="button"].button-primary { - color: #FFF; - background-color: #33C3F0; - border-color: #33C3F0; } -.button.button-primary:hover, -button.button-primary:hover, -input[type="submit"].button-primary:hover, -input[type="reset"].button-primary:hover, -input[type="button"].button-primary:hover, -.button.button-primary:focus, -button.button-primary:focus, -input[type="submit"].button-primary:focus, -input[type="reset"].button-primary:focus, -input[type="button"].button-primary:focus { - color: #FFF; - background-color: #1EAEDB; - border-color: #1EAEDB; } - - -/* Forms -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -input[type="email"], -input[type="number"], -input[type="search"], -input[type="text"], -input[type="tel"], -input[type="url"], -input[type="password"], -textarea, -select { - height: 38px; - padding: 6px 10px; /* The 6px vertically centers text on FF, ignored by Webkit */ - background-color: #fff; - border: 1px solid #D1D1D1; - border-radius: 4px; - box-shadow: none; - box-sizing: border-box; } -/* Removes awkward default styles on some inputs for iOS */ -input[type="email"], -input[type="number"], -input[type="search"], -input[type="text"], -input[type="tel"], -input[type="url"], -input[type="password"], -textarea { - -webkit-appearance: none; - -moz-appearance: none; - appearance: none; } -textarea { - min-height: 65px; - padding-top: 6px; - padding-bottom: 6px; } -input[type="email"]:focus, -input[type="number"]:focus, -input[type="search"]:focus, -input[type="text"]:focus, -input[type="tel"]:focus, -input[type="url"]:focus, -input[type="password"]:focus, -textarea:focus, -select:focus { - border: 1px solid #33C3F0; - outline: 0; } -label, -legend { - display: block; - margin-bottom: .5rem; - font-weight: 600; } -fieldset { - padding: 0; - border-width: 0; } -input[type="checkbox"], -input[type="radio"] { - display: inline; } -label > .label-body { - display: inline-block; - margin-left: .5rem; - font-weight: normal; } - - -/* Lists -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -ul { - list-style: circle inside; } -ol { - list-style: decimal inside; } -ol, ul { - padding-left: 0; - margin-top: 0; } -ul ul, -ul ol, -ol ol, -ol ul { - margin: 1.5rem 0 1.5rem 3rem; - font-size: 90%; } -li { - margin-bottom: 1rem; } - - -/* Code -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -code { - padding: .2rem .5rem; - margin: 0 .2rem; - font-size: 90%; - white-space: nowrap; - background: #F1F1F1; - border: 1px solid #E1E1E1; - border-radius: 4px; } -pre > code { - display: block; - padding: 1rem 1.5rem; - white-space: pre; } - - -/* Tables -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -th, -td { - padding: 12px 15px; - text-align: left; - border-bottom: 1px solid #E1E1E1; } - -/*th:first-child, -td:first-child { - padding-left: 0; } -th:last-child, -td:last-child { - padding-right: 0; } -*/ - -/* Spacing -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -button, -.button { - margin-bottom: 1rem; } -input, -textarea, -select, -fieldset { - margin-bottom: 1.5rem; } -pre, -blockquote, -dl, -figure, -table, -p, -ul, -ol, -form { - margin-bottom: 2.5rem; } - - -/* Utilities -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -.u-full-width { - width: 100%; - box-sizing: border-box; } -.u-max-full-width { - max-width: 100%; - box-sizing: border-box; } -.u-pull-right { - float: right; } -.u-pull-left { - float: left; } - - -/* Misc -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -hr { - margin-top: 3rem; - margin-bottom: 3.5rem; - border-width: 0; - border-top: 1px solid #E1E1E1; } - - -/* Clearing -–––––––––––––––––––––––––––––––––––––––––––––––––– */ - -/* Self Clearing Goodness */ -.container:after, -.row:after, -.u-cf { - content: ""; - display: table; - clear: both; } - - -/* Media Queries -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -/* -Note: The best way to structure the use of media queries is to create the queries -near the relevant code. For example, if you wanted to change the styles for buttons -on small devices, paste the mobile query code up in the buttons section and style it -there. -*/ - - -/* Larger than mobile */ -@media (min-width: 400px) {} - -/* Larger than phablet (also point when grid becomes active) */ -@media (min-width: 550px) {} - -/* Larger than tablet */ -@media (min-width: 750px) {} - -/* Larger than desktop */ -@media (min-width: 1000px) {} - -/* Larger than Desktop HD */ -@media (min-width: 1200px) {}
--- a/riboplot/data/js/custom.js Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -$(document).ready(function() -{ - $("#counts-table").tablesorter({sortList: [[2,1]]}); - //assign the sortStart event - $("#counts-table").bind("sortStart", function() { - $("#overlay").show(); - }).bind("sortEnd",function() { - $("#overlay").hide(); - }); -} -);
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\ No newline at end of file
--- a/riboplot/data/js/jquery.tablesorter.min.js Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - -(function($){$.extend({tablesorter:new -function(){var parsers=[],widgets=[];this.defaults={cssHeader:"header",cssAsc:"headerSortUp",cssDesc:"headerSortDown",cssChildRow:"expand-child",sortInitialOrder:"asc",sortMultiSortKey:"shiftKey",sortForce:null,sortAppend:null,sortLocaleCompare:true,textExtraction:"simple",parsers:{},widgets:[],widgetZebra:{css:["even","odd"]},headers:{},widthFixed:false,cancelSelection:true,sortList:[],headerList:[],dateFormat:"us",decimal:'/\.|\,/g',onRenderHeader:null,selectorHeaders:'thead th',debug:false};function benchmark(s,d){log(s+","+(new Date().getTime()-d.getTime())+"ms");}this.benchmark=benchmark;function log(s){if(typeof console!="undefined"&&typeof console.debug!="undefined"){console.log(s);}else{alert(s);}}function buildParserCache(table,$headers){if(table.config.debug){var parsersDebug="";}if(table.tBodies.length==0)return;var rows=table.tBodies[0].rows;if(rows[0]){var list=[],cells=rows[0].cells,l=cells.length;for(var i=0;i<l;i++){var p=false;if($.metadata&&($($headers[i]).metadata()&&$($headers[i]).metadata().sorter)){p=getParserById($($headers[i]).metadata().sorter);}else if((table.config.headers[i]&&table.config.headers[i].sorter)){p=getParserById(table.config.headers[i].sorter);}if(!p){p=detectParserForColumn(table,rows,-1,i);}if(table.config.debug){parsersDebug+="column:"+i+" parser:"+p.id+"\n";}list.push(p);}}if(table.config.debug){log(parsersDebug);}return list;};function detectParserForColumn(table,rows,rowIndex,cellIndex){var l=parsers.length,node=false,nodeValue=false,keepLooking=true;while(nodeValue==''&&keepLooking){rowIndex++;if(rows[rowIndex]){node=getNodeFromRowAndCellIndex(rows,rowIndex,cellIndex);nodeValue=trimAndGetNodeText(table.config,node);if(table.config.debug){log('Checking if value was empty on 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--- a/riboplot/data/ribocount.html Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,63 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> -<head> - - <!-- Basic Page Needs - –––––––––––––––––––––––––––––––––––––––––––––––––– --> - <meta charset="utf-8"> - <title>Ribo-Seq profile counts</title> - <meta name="description" content=""> - <meta name="author" content=""> - - <!-- Mobile Specific Metas - –––––––––––––––––––––––––––––––––––––––––––––––––– --> - <meta name="viewport" content="width=device-width, initial-scale=1"> - - <!-- FONT - –––––––––––––––––––––––––––––––––––––––––––––––––– --> - <!--<link href="http://fonts.googleapis.com/css?family=Open+Sans:400,300,600"--> - <!--rel="stylesheet" type="text/css">--> - - <!-- CSS - –––––––––––––––––––––––––––––––––––––––––––––––––– --> - <link rel="stylesheet" href="css/normalize.css"> - <link rel="stylesheet" href="css/skeleton.css"> - <link rel="stylesheet" href="css/custom.css"> - - <!-- Favicon - –––––––––––––––––––––––––––––––––––––––––––––––––– --> - <link rel="icon" type="image/png" href="images/favicon.png"> - -</head> -<body> - -<!-- Primary Page Layout -–––––––––––––––––––––––––––––––––––––––––––––––––– --> -<div class="container"> - <div class="row"> - <div class="twelve columns"> - <h3 id="page-title">Ribo-Seq profile counts for all transcripts</h3> - <h5>Total transcript(s) <span class="info">{count}</span>, Footprint - length <span class="info">{length}</span></h5> - <div id="overlay">Sorting this large table...</div> - <table id="counts-table" class="tablesorter u-full-width"> - <thead> - <tr> - <th>Number</th> - <th>Transcript name</th> - <th>Total reads</th> - <th>Counts (csv file)</th> - </tr> - </thead> - <tbody> - {table_content} - </tbody> - </table> - </div> - </div> -</div> -<script type="text/javascript" src="js/jquery-1.11.3.min.js"></script> -<script type="text/javascript" src="js/jquery.tablesorter.min.js"></script> -<script type="text/javascript" src="js/custom.js"></script> -</body> -</html>
--- a/riboplot/data/ribocount_index.html Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> -<head> - - <!-- Basic Page Needs - –––––––––––––––––––––––––––––––––––––––––––––––––– --> - <meta charset="utf-8"> - <title>Ribo-Seq profile counts</title> - - <!-- Mobile Specific Metas - –––––––––––––––––––––––––––––––––––––––––––––––––– --> - <meta name="viewport" content="width=device-width, initial-scale=1"> -</head> -<body> - -<h3>Ribocount output</h3> -<h5>The following zip file contains read counts as CSV files for <em>{count}</em> -transcripts with read length <em>{read_length}</em>.</h5> - -<p>Download: <a href="ribocount_output.zip">ribocount_output.zip</a></p> - -<p>Note: To view the list of transcripts and their read counts (in CSV), -extract the zip file and open "index.html" in a web browser. </p> -</body> -</html> \ No newline at end of file
--- a/riboplot/data/riboplot.html Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> -<head> - - <!-- Basic Page Needs - –––––––––––––––––––––––––––––––––––––––––––––––––– --> - <meta charset="utf-8"> - <title>Ribo-Seq profile plot</title> - <meta name="description" content=""> - <meta name="author" content=""> - - <!-- Mobile Specific Metas - –––––––––––––––––––––––––––––––––––––––––––––––––– --> - <meta name="viewport" content="width=device-width, initial-scale=1"> - - <!-- FONT - –––––––––––––––––––––––––––––––––––––––––––––––––– --> - <!--<link href="http://fonts.googleapis.com/css?family=Open+Sans:400,300,600"--> - <!--rel="stylesheet" type="text/css">--> - - <!-- CSS - –––––––––––––––––––––––––––––––––––––––––––––––––– --> - <link rel="stylesheet" href="css/normalize.css"> - <link rel="stylesheet" href="css/skeleton.css"> - <link rel="stylesheet" href="css/custom.css"> - - <!-- Favicon - –––––––––––––––––––––––––––––––––––––––––––––––––– --> - <link rel="icon" type="image/png" href="images/favicon.png"> - -</head> -<body> - -<!-- Primary Page Layout -–––––––––––––––––––––––––––––––––––––––––––––––––– --> -<div class="container"> - <div class="row"> - <div id="main" class="twelve columns"> - <center> - <h3>Ribo-Seq profile plot</h3> - <p> - <img width="100%" class="u-max-full-width" src="riboplot.png"/><br> - <p> - <h5>Download plots<br> - <a href="riboplot.png">PNG</a>, <a href="riboplot.svg">SVG</a> - </h5> - - <h5>Download counts<br> - <a href="RiboCounts.csv">RiboCounts.csv</a> - </h5> - <p> - <small> - (Right click --> Save link/target as...) - </small> - </p> - </center> - </div> - </div> -</div> -</body> -</html> \ No newline at end of file
--- a/riboplot/ribocore.py Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,235 +0,0 @@ -"""Common functions. """ -import pysam -import logging -import subprocess - - -# create logger for the entire program -log = logging.getLogger('riboplot') -log.setLevel(logging.DEBUG) - -# create console handler with a higher log level -ch = logging.StreamHandler() -ch.setLevel(logging.INFO) - -formatter = logging.Formatter('%(asctime)s - %(module)s %(levelname)s %(message)s', datefmt='%Y-%m-%d %H:%M:%S') -ch.setFormatter(formatter) -log.addHandler(ch) - - -class ArgumentError(Exception): - """Raised when invalid arguments are sent in the command line.""" - pass - - -class RiboPlotError(Exception): - """General errors relating to riboplot.""" - pass - - -class RiboCountError(Exception): - """General errors relating to ribocount.""" - pass - - -class RNACountsError(Exception): - """For errors related to RNA Coverage generation using bedtools. """ - pass - - -def is_bam_valid(bam_file): - """Check if bam file is valid. Raises a ValueError if pysam cannot read the file. - - #TODO: pysam does not differentiate between BAM and SAM - """ - try: - f = pysam.AlignmentFile(bam_file) - except ValueError: - raise - except: - raise - else: - f.close() - - return True - - -def bam_has_index(bam_file): - """Check if bam file has an index. Returns True/False.""" - has_index = None - with pysam.AlignmentFile(bam_file, 'rb') as bam_fileobj: - try: - bam_fileobj.fetch(bam_fileobj.references[0]) - except ValueError as err: - if err.message == 'fetch called on bamfile without index': - bam_fileobj.close() - has_index = False - else: - has_index = True - return has_index - - -def create_bam_index(bam_file): - """Create an index for the given BAM file.""" - pysam.index(bam_file) - - -def get_bam_read_lengths(bam_file): - """For a given BAM file, return an unique list of read lengths present.""" - read_lengths = [] - with pysam.AlignmentFile(bam_file, 'rb') as bam_fileobj: - for record in bam_fileobj: - read_lengths.append(record.query_length) - return set(read_lengths) - - -def is_fasta_valid(fasta_file): - """Check if fasta file is valid. Raises a ValueError if pysam cannot read the file. - - #TODO: pysam does not differentiate between BAM and SAM - """ - try: - f = pysam.FastaFile(fasta_file) - except IOError: - raise - else: - f.close() - return True - - -def get_fasta_record(fasta): - """Return a single transcript name from a valid fasta file""" - f = pysam.FastaFile(fasta) - transcript = f.references[0] - f.close() - return transcript - - -def get_fasta_records(fasta, transcripts): - """Return list of transcript records from the given fasta file. - Each record will be of the form {'sequence_id': {'sequence': 'AAA', 'length': 3}} - - trascripts should be provided as a list of sequence id's. - - """ - records = {} - f = pysam.FastaFile(fasta) - for transcript in transcripts: - try: - sequence, length = f.fetch(transcript), f.get_reference_length(transcript) - except KeyError: - msg = 'Transcript "{}" does not exist in transcriptome FASTA file'.format(transcript) - log.error(msg) - raise ArgumentError(msg) - records[transcript] = {'sequence': sequence, 'length': length} - f.close() - return records - - -def get_ribo_counts(ribo_fileobj, transcript_name, read_length=0): - """Get total reads and read counts in all 3 frames for the give transcript - from input BAM file (indexed). - - """ - read_counts = {} - total_reads = 0 - - for record in ribo_fileobj.fetch(transcript_name): - if read_length: - if record.query_length != read_length: - continue - total_reads += 1 - position = record.pos + 1 - - try: - read_counts[position] - except KeyError: - read_counts[position] = {1: 0, 2: 0, 3: 0} - - rem = position % 3 - if rem == 0: - read_counts[position][3] += 1 - else: - read_counts[position][rem] += 1 - - return read_counts, total_reads - - -def check_required_arguments(ribo_file, transcriptome_fasta, transcript_name=None): - """Check required arguments of both riboplot and ribocount.""" - # Is this a valid BAM file? i.e., can pysam read it? - try: - is_bam_valid(ribo_file) - except ValueError: - log.error('The given RiboSeq BAM file is not valid') - raise - - # Does the BAM file have an index? If not, create it. - if not bam_has_index(ribo_file): - log.info('Creating an index for the BAM file...') - create_bam_index(ribo_file) - - # Is FASTA file valid? - fasta_valid = False - try: - fasta_valid = is_fasta_valid(transcriptome_fasta) - except IOError: - log.error('Transcriptome FASTA file is not valid') - raise - - if fasta_valid: - if transcript_name: - try: - get_fasta_records(transcriptome_fasta, [transcript_name]) - except IOError: - log.error('Could not get FASTA sequence of "{}" from transcriptome FASTA file'.format(transcript_name)) - raise - else: - # ribocount doesn't have a transcript option so we get the first - # sequence name from the fasta file - transcript_name = get_fasta_record(transcriptome_fasta) - - # check if transcript also exists in BAM - with pysam.AlignmentFile(ribo_file, 'rb') as bam_file: - if transcript_name not in bam_file.references: - msg = 'Transcript "{}" does not exist in BAM file'.format(transcript_name) - log.error(msg) - raise ArgumentError(msg) - - -def check_optional_arguments(ribo_file, read_length=None, read_offset=None, rna_file=None): - """Check all optional arguments.""" - if rna_file: - try: - subprocess.check_output(['bedtools', '--version']) - except OSError: - log.error('Could not find bedtools in PATH. bedtools is required' - 'for generating RNA coverage plot.') - raise - # Is this a valid BAM file? i.e., can pysam read it? - try: - is_bam_valid(rna_file) - except ValueError: - log.error('The given RNASeq BAM file is not valid') - raise - - # If read_length is given, it must be a positive integer or reads of that - # length must exist in the BAM file - if read_length: - if read_length < 0: - msg = 'Read length must be a positive value' - log.error(msg) - raise ArgumentError(msg) - - bam_read_lengths = get_bam_read_lengths(ribo_file) - if read_length not in bam_read_lengths: - msg = 'Reads of the length "{}" does not exist in the BAM file'.format(read_length) - log.error(msg) - raise ArgumentError(msg) - - # If read_offset is given, it must be a positive integer - if read_offset: - if read_offset < 0: - msg = 'Read offset must be 0 or greater' - log.error(msg) - raise ArgumentError(msg)
--- a/riboplot/ribocount.py Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,168 +0,0 @@ -# -*- coding: utf-8 -*- -"""ribocount""" -import sys - -# check dependencies -try: - import pysam -except ImportError as e: - sys.exit('Could not import the "pysam" module\n\nImporting failed with' - '{}\n\n'.format(e)) - -import os -# import timeit -import shutil -import zipfile -import logging -import argparse - -import ribocore -import config - -# Default is production -CONFIG = config.ProductionConfig() - -log = logging.getLogger('riboplot') - - -class ErrorLogFormatter(logging.Formatter): - """Custom error log format for the HTML file""" - - def format(self, record): - return '<h2>RiboCount Error</h2><p>{}</p>'.format(record.msg) - - -def create_parser(): - """Argument parser. """ - parser = argparse.ArgumentParser( - prog='ribocount.py', description='Output read counts for all transcripts') - - # required arguments - required = parser.add_argument_group('required arguments') - required.add_argument('-b', '--ribo_file', help='Ribo-Seq alignment file in BAM format', required=True) - required.add_argument('-f', '--transcriptome_fasta', help='FASTA format file of the transcriptome', required=True) - - # optional arguments - parser.add_argument('-l', '--read_length', help='Read length to consider (default: %(default)s)', - metavar='INTEGER', type=int) - parser.add_argument('-s', '--read_offset', help='Read offset (default: %(default)s)', - metavar='INTEGER', type=int, default=0) - parser.add_argument('-m', '--html_file', help='Output file for results (HTML)', default='ribocount.html') - parser.add_argument('-o', '--output_path', help='Files are saved in this directory', default='output') - parser.add_argument('-d', '--debug', help='Flag. Produce debug output', action='store_true') - - return parser - - -def main(args): - """Main program""" - (ribo_file, transcriptome_fasta, read_length, read_offset, output_path, html_file) = ( - args.ribo_file, args.transcriptome_fasta, args.read_length, - args.read_offset, args.output_path, args.html_file) - - log.debug('Supplied arguments\n{}'.format( - '\n'.join(['{:<20}: {}'.format(k, v) for k, v in vars(args).items()]))) - - # error messages (simple format) are written to html file - fh = logging.FileHandler(html_file) - fh.setLevel(logging.ERROR) - fh.setFormatter(ErrorLogFormatter('%(message)s')) - log.addHandler(fh) - - log.info('Checking if required arguments are valid...') - ribocore.check_required_arguments(ribo_file=ribo_file, transcriptome_fasta=transcriptome_fasta) - log.info('Done') - - log.info('Checking if optional arguments are valid...') - ribocore.check_optional_arguments(ribo_file=ribo_file, read_length=read_length, read_offset=read_offset) - log.info('Done') - - if not os.path.exists(output_path): - os.mkdir(output_path) - - # zip_dir contents will be written here and a zip archive will be created - # from this directory - zip_dir = os.path.join(output_path, 'ribocount_output') - if not os.path.exists(zip_dir): - os.mkdir(zip_dir) - - csv_dir = os.path.join(zip_dir, 'csv') - if not os.path.exists(csv_dir): - os.mkdir(csv_dir) - - count = 0 - table_content = '' - bam_fileobj = pysam.AlignmentFile(ribo_file, 'rb') - fasta_file = pysam.FastaFile(transcriptome_fasta) - log.info('Get RiboSeq read counts for all transcripts in FASTA') - for transcript in fasta_file.references: - rp_counts, rp_reads = ribocore.get_ribo_counts(bam_fileobj, transcript, read_length) - if not rp_reads: # no reads for this transcript. skip. - continue - - log.debug('Writing counts for {}'.format(transcript)) - count += 1 - csv_file = 'RiboCounts{}.csv'.format(count) - with open(os.path.join(csv_dir, csv_file), 'w') as f: - f.write('"Position","Frame 1","Frame 2","Frame 3"\n') - - for pos in range(1, len(fasta_file[transcript]) + 1): - if pos in rp_counts: - f.write('{0},{1},{2},{3}\n'.format( - pos, rp_counts[pos][1], rp_counts[pos][2], rp_counts[pos][3])) - else: - f.write('{0},{1},{2},{3}\n'.format(pos, 0, 0, 0)) - table_content += ('<tr><td>{0}</td><td>{1}</td><td>{2}</td><td><a href="csv/{3}">' - '{3}</a></td></tr>'.format(count, transcript, rp_reads, csv_file)) - fasta_file.close() - bam_fileobj.close() - - # only for display in HTML - if not read_length: - read_length = 'All' - - log.info('Done') - - if not count: - if read_length: - log.info('No transcripts found for read length {}'.format(read_length)) - else: - log.info('No transcripts found') - else: - with open(os.path.join(CONFIG.PKG_DATA_DIR, 'ribocount.html')) as g,\ - open(os.path.join(zip_dir, 'index.html'), 'w') as h: - h.write(g.read().format(count=count, length=read_length, table_content=table_content)) - - for asset in ('css', 'js'): - asset_dir = os.path.join(zip_dir, asset) - if not os.path.exists(asset_dir): - os.mkdir(asset_dir) - asset_data_dir = os.path.join(CONFIG.PKG_DATA_DIR, asset) - for fname in os.listdir(asset_data_dir): - shutil.copy(os.path.join(asset_data_dir, fname), - os.path.join(zip_dir, asset, fname)) - - log.info('Creating zip file') - os.chdir(output_path) - with zipfile.ZipFile('ribocount_output.zip', 'w') as zipf: - for root, d, f in os.walk('ribocount_output'): - for name in f: - zipf.write(os.path.join(root, name)) - shutil.rmtree('ribocount_output') - os.chdir('../') - log.debug('Writing HTML report') - - with open(os.path.join(CONFIG.PKG_DATA_DIR, 'ribocount_index.html')) as j, open(args.html_file, 'w') as k: - k.write(j.read().format(count=count, read_length=read_length)) - log.info('Finished') - - -def run(): - """Run program""" - parsed = create_parser() - args = parsed.parse_args() - main(args) - - -if __name__ == '__main__': - run()
--- a/riboplot/riboplot.py Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,354 +0,0 @@ -# -*- coding: utf-8 -*- -import sys - -# check dependencies -module_errors = {} -try: - import pysam -except ImportError as e: - module_errors['pysam'] = str(e) - -try: - from matplotlib import pyplot as plt -except ImportError as e: - module_errors['matplotlib'] = str(e) -else: - from matplotlib import gridspec - from matplotlib.font_manager import FontProperties - -if len(module_errors): - msg = 'Could not import all required modules:\n\n' - for module, error in module_errors.items(): - msg += 'Importing "{0}" failed with \n{1}\n\n'.format(module, error) - sys.exit(msg) - -import os -import re -import config -# import timeit -import shutil -import logging -import tempfile -import argparse -import subprocess - -import ribocore -# Default is production -CONFIG = config.ProductionConfig() - -# create logger -log = logging.getLogger('riboplot') - - -class ErrorLogFormatter(logging.Formatter): - """Custom error log format for the HTML file""" - - def format(self, record): - return '<h2>RiboPlot Error</h2><p>{}</p>'.format(record.msg) - - -def get_start_stops(transcript_sequence, start_codons=None, stop_codons=None): - """Return start and stop positions for all frames in the given - transcript. - - """ - if not start_codons: - start_codons = ['ATG'] - if not stop_codons: - stop_codons = ['TAA', 'TAG', 'TGA'] - - seq_frames = {1: {'starts': [], 'stops': []}, - 2: {'starts': [], 'stops': []}, - 3: {'starts': [], 'stops': []}} - - for codons, positions in ((start_codons, 'starts'), - (stop_codons, 'stops')): - if len(codons) > 1: - pat = re.compile('|'.join(codons)) - else: - pat = re.compile(codons[0]) - - for m in re.finditer(pat, transcript_sequence): - # Increment position by 1, Frame 1 starts at position 1 not 0 - start = m.start() + 1 - rem = start % 3 - if rem == 1: # frame 1 - seq_frames[1][positions].append(start) - elif rem == 2: # frame 2 - seq_frames[2][positions].append(start) - elif rem == 0: # frame 3 - seq_frames[3][positions].append(start) - return seq_frames - - -def get_rna_counts(rna_file, transcript_name): - """Get coverage for a given RNA BAM file, return read counts. """ - # check if the RNA file exists - if not os.path.exists(rna_file): - msg = 'RNA-Seq BAM file "{}" does not exist'.format(rna_file) - logging.error(msg) - raise OSError(msg) - rna_counts = {} - - cov_file = tempfile.NamedTemporaryFile(delete=False) - try: - subprocess.check_call( - ['bedtools', 'genomecov', '-ibam', rna_file, - '-bg'], stdout=cov_file) - except subprocess.CalledProcessError as e: - # needs testing - raise ribocore.RNACountsError('Could not generate coverage for RNA BAM file. \n{}\n'.format(e)) - for line in open(cov_file.name): - line = line.split() - if line[0] == transcript_name: - position, count = int(line[1]) + 1, int(line[3]) - rna_counts[position] = count - cov_file.close() - os.unlink(cov_file.name) - return rna_counts - - -def set_axis_color(axis, color): - """Sets the spine color of all sides of an axis (top, right, bottom, left).""" - axis.spines['top'].set_color(color) - axis.spines['right'].set_color(color) - axis.spines['bottom'].set_color(color) - axis.spines['left'].set_color(color) - - -def plot_profile(ribo_counts, transcript_name, transcript_length, - start_stops, read_length=None, read_offset=None, rna_counts=None, - html_file='index.html', output_path='output'): - """Plot read counts (in all 3 frames) and RNA coverage if provided for a - single transcript. - - """ - gs = gridspec.GridSpec(6, 1, height_ratios=[0.1, 6.8, 0.1, 1, 1, 1], hspace=0.35) - font_xsmall = {'family': 'sans-serif', 'color': '#555555', 'weight': 'normal', 'size': 'x-small'} - - # plot for frames legend - ax1 = plt.subplot(gs[0], axisbg='white') - ax1.text(0.95, 0.1, "frame 1", size=6, ha="right", va="center", color='white', - bbox=dict(boxstyle="square", color='tomato')) - ax1.text(0.97, 0.1, "2", size=6, ha="right", va="center", color='white', - bbox=dict(boxstyle="square", color='limegreen')) - ax1.text(0.99, 0.1, "3", size=6, ha="right", va="center", color='white', - bbox=dict(boxstyle="square", color='deepskyblue')) - - # riboseq bar plots - ax2 = plt.subplot(gs[1]) - label = 'Ribo-Seq count' - if read_length: - label = 'Ribo-Seq count ({}-mer)'.format(read_length) - ax2.set_ylabel(label, fontdict=font_xsmall, labelpad=10) - - # rna coverage if available - ax_rna = None - if rna_counts: - ax_rna = ax2.twinx() - ax_rna.set_ylabel('RNA-Seq count', fontdict=font_xsmall, labelpad=10) - ax_rna.bar(rna_counts.keys(), rna_counts.values(), facecolor='#e6e6e6', edgecolor='#e6e6e6', label='RNA', linewidth=0.5) - ax_rna.set_zorder(1) - - frame_counts = {1: {}, 2: {}, 3: {}} - for k, v in ribo_counts.iteritems(): - for fr in (1, 2, 3): - if v[fr] > 0: - frame_counts[fr][k] = v[fr] - break - - cnts = [] - [cnts.extend(item.values()) for item in frame_counts.values()] - y_max = int(round(max(cnts) * 1.2)) - ax2.set_ylim(0.0, y_max) - ax2.set_zorder(2) - ax2.patch.set_facecolor('none') - - for frame, color in ((1, 'tomato'), (2, 'limegreen'), (3, 'deepskyblue')): - if read_offset: - x_vals = [pos + read_offset for pos in frame_counts[frame].keys()] - else: - x_vals = frame_counts[frame].keys() - ax2.bar(x_vals, frame_counts[frame].values(), color=color, facecolor=color, edgecolor=color, linewidth=0.5) - - ax3 = plt.subplot(gs[2], axisbg='white') - ax3.text(0.90, 0.1, "start codon", size=6, ha="right", va="center", color='#555555', - bbox=dict(boxstyle="square", facecolor='white', edgecolor='#c6c6c6')) - ax3.text(0.99, 0.1, "stop codon", size=6, ha="right", va="center", color='white', - bbox=dict(boxstyle="square", color='#777777')) - - ax4 = plt.subplot(gs[3], sharex=ax2, axisbg='#c6c6c6') - ax5 = plt.subplot(gs[4], sharex=ax2, axisbg='#c6c6c6') - ax6 = plt.subplot(gs[5], sharex=ax2, axisbg='#c6c6c6') - - for axis in (ax1, ax3): - axis.tick_params(top=False, left=False, right=False, bottom=False, labeltop=False, - labelleft=False, labelright=False, labelbottom=False) - set_axis_color(axis, 'white') - - axes = [ax2] - if ax_rna: - axes.append(ax_rna) - - fp = FontProperties(size='5') - for axis in axes: - set_axis_color(axis, '#f7f7f7') - for item in (axis.get_xticklabels() + axis.get_yticklabels()): - item.set_fontproperties(fp) - item.set_color('#555555') - - for axis, frame in ((ax4, 1), (ax5, 2), (ax6, 3)): - set_axis_color(axis, '#C6C6C6') - for item in (axis.get_xticklabels()): - item.set_fontproperties(fp) - item.set_color('#555555') - axis.set_ylim(0, 0.2) - axis.set_xlim(0, transcript_length) - starts = [(item, 1) for item in start_stops[frame]['starts']] - stops = [(item, 1) for item in start_stops[frame]['stops']] - start_colors = ['#ffffff' for item in starts] - axis.broken_barh(starts, (0.11, 0.2), - facecolors=start_colors, edgecolors=start_colors, label='start', zorder=5, linewidth=0.5) - stop_colors = ['#777777' for item in stops] - axis.broken_barh(stops, (0, 0.2), facecolors=stop_colors, - edgecolors=stop_colors, label='stop', zorder=5, linewidth=0.5) - axis.set_ylabel('{}'.format(frame), - fontdict={'family': 'sans-serif', 'color': '#555555', - 'weight': 'normal', 'size': '6'}, - rotation='horizontal', labelpad=10, verticalalignment='center') - axis.tick_params(top=False, left=False, right=False, labeltop=False, - labelleft=False, labelright=False, direction='out') - plt.xlabel('Transcript length ({} nt)'.format(transcript_length), fontdict=font_xsmall, labelpad=10) - plt.title('Transcript {}'.format(transcript_name), - fontdict={'family': 'sans-serif', 'color': '#222222', - 'weight': 'normal', 'size': 'x-small'}, y=13.0) - if not os.path.exists(output_path): - os.mkdir(output_path) - plt.savefig(os.path.join(output_path, 'riboplot.svg')) - plt.savefig(os.path.join(output_path, 'riboplot.png'), dpi=300) - - with open(os.path.join(CONFIG.PKG_DATA_DIR, 'riboplot.html')) as g, open(os.path.join(output_path, html_file), 'w') as h: - h.write(g.read().format(transcript_name=transcript_name)) - - css_dir = os.path.join(output_path, 'css') - if not os.path.exists(css_dir): - os.mkdir(css_dir) - - css_data_dir = os.path.join(CONFIG.PKG_DATA_DIR, 'css') - for fname in os.listdir(css_data_dir): - shutil.copy(os.path.join(css_data_dir, fname), os.path.join(output_path, 'css', fname)) - - -def create_parser(): - """Argument parser. """ - parser = argparse.ArgumentParser( - prog='riboplot.py', description='Plot and output read counts for a single transcript') - - required = parser.add_argument_group('required arguments') - required.add_argument('-b', '--ribo_file', help='Ribo-Seq alignment file in BAM format', required=True) - required.add_argument('-f', '--transcriptome_fasta', help='FASTA format file of the transcriptome', required=True) - required.add_argument('-t', '--transcript_name', help='Transcript name', metavar='TEXT', required=True) - - # plot function - optional arguments - parser.add_argument('-n', '--rna_file', help='RNA-Seq alignment file (BAM)') - parser.add_argument('-l', '--read_length', help='Read length to consider (default: %(default)s)', - metavar='INTEGER', type=int) - parser.add_argument('-s', '--read_offset', help='Read offset (default: %(default)s)', - metavar='INTEGER', type=int, default=0) - parser.add_argument('-m', '--html_file', help='Output file for results (HTML)', default='riboplot.html') - parser.add_argument('-o', '--output_path', help='Files are saved in this directory', default='output') - parser.add_argument('-d', '--debug', help='Flag. Produce debug output', action='store_true') - - return parser - - -def main(args): - """Main program""" - (ribo_file, rna_file, transcript_name, transcriptome_fasta, read_length, - read_offset, output_path, html_file) = ( - args.ribo_file, args.rna_file, args.transcript_name, args.transcriptome_fasta, - args.read_length, args.read_offset, args.output_path, args.html_file) - - log.debug('Supplied arguments\n{}'.format( - '\n'.join(['{:<20}: {}'.format(k, v) for k, v in vars(args).items()]))) - - # error messages (simple format) are written to html file - fh = logging.FileHandler(html_file) - fh.setLevel(logging.ERROR) - fh.setFormatter(ErrorLogFormatter('%(message)s')) - log.addHandler(fh) - - log.info('Checking if required arguments are valid...') - ribocore.check_required_arguments(ribo_file=ribo_file, transcriptome_fasta=transcriptome_fasta, - transcript_name=transcript_name) - log.info('Done') - - log.info('Checking if optional arguments are valid...') - ribocore.check_optional_arguments(ribo_file=ribo_file, read_length=read_length, read_offset=read_offset, - rna_file=rna_file) - log.info('Done') - - log.info('Get ribo-seq read counts and total reads in Ribo-Seq...') - bam_fileobj = pysam.AlignmentFile(ribo_file, 'rb') - ribo_counts, total_reads = ribocore.get_ribo_counts(bam_fileobj, transcript_name, read_length) - bam_fileobj.close() - - if not ribo_counts: - msg = ('No RiboSeq read counts for transcript {}. No plot will be ' - 'generated!'.format(transcript_name)) - log.error(msg) - raise ribocore.RiboPlotError(msg) - else: - log.info('Get RNA counts for the given transcript...') - mrna_counts = {} - if rna_file: - try: - mrna_counts = get_rna_counts(rna_file, transcript_name) - except OSError as e: - log.error(e) - raise - - if not mrna_counts: - log.warn('No RNA counts for this transcript from the given RNA Seq file. ' - 'RNA-Seq coverage will not be generated') - else: - log.debug('No RNA-Seq data provided. Not generating coverage') - - log.info('Get sequence and length of the given transcripts from FASTA file...') - fasta_records = ribocore.get_fasta_records(transcriptome_fasta, [transcript_name]) - transcript_seq, transcript_length = (fasta_records[transcript_name]['sequence'], - fasta_records[transcript_name]['length']) - - log.info('Get start/stop positions in transcript sequence (3 frames)...') - codon_positions = get_start_stops(transcript_seq) - - if not os.path.exists(output_path): - os.mkdir(output_path) - - log.info('Writing RiboSeq read counts for {}'.format(transcript_name)) - with open(os.path.join(output_path, 'RiboCounts.csv'), 'w') as f: - f.write('"Position","Frame 1","Frame 2","Frame 3"\n') - - for pos in range(1, transcript_length + 1): - if pos in ribo_counts: - f.write('{0},{1},{2},{3}\n'.format( - pos, ribo_counts[pos][1], ribo_counts[pos][2], ribo_counts[pos][3])) - else: - f.write('{0},{1},{2},{3}\n'.format(pos, 0, 0, 0)) - - log.info('Generating RiboPlot...') - plot_profile(ribo_counts, transcript_name, transcript_length, - codon_positions, read_length, read_offset, mrna_counts, - html_file=args.html_file, output_path=args.output_path) - log.info('Finished!') - - -def run(): - """Run program""" - parsed = create_parser() - args = parsed.parse_args() - main(args) - - -if __name__ == '__main__': - run()
--- a/riboplot/scripts/run_coverage.sh Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -#!/bin/bash -# Run coverage and geneated HTML reports -echo "INFO: If this fails with command not found, please install the coverage python package and re-run" -coverage run --source tests/test_riboplot.py --source riboplot setup.py test -coverage html
--- a/riboplot/scripts/run_ribocount_sample.sh Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -#!/bin/bash -# A sample ribocount run with a Ribo-Seq sorted BAM format alignment -# and a FASTA file of the transcriptome. -echo "Please run this script from the main package directory else this would fail" -ribocount -b tests/data/5hRPFsorted.bam -f tests/data/zebrafish.fna -
--- a/riboplot/scripts/run_riboplot_sample.sh Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -#!/bin/bash -# A sample riboplot run with a sorted Ribo-Seq BAM file, FASTA file of -# the transcriptome and a transcript. - -echo "Please run this script from the main package directory else this would fail" -riboplot -b tests/data/5hRPFsorted.bam -f tests/data/zebrafish.fna \ - -t 'gi|148357119|ref|NM_001098396.1|' -n tests/data/5hmRNAsorted.bam -
--- a/riboplot/scripts/run_tests.sh Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -#!/bin/bash -# Run all tests - -echo "Please run this script from the main package directory else this would fail" -python setup.py test
--- a/setup.cfg Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -[wheel] -universal = 1 - -[pep8] -ignore = E501 -max-line-length = 160
--- a/setup.py Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,59 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - - -try: - from setuptools import setup -except ImportError: - from distutils.core import setup - - -with open('README.rst') as readme_file: - readme = readme_file.read() - -with open('HISTORY.rst') as history_file: - history = history_file.read().replace('.. :changelog:', '') - -requirements = ['matplotlib==1.3.1', 'pysam==0.8.3'] - -test_requirements = [ - # TODO: put package test requirements here -] - -setup( - name='riboplot', - version='0.1.0', - description="Plot read counts of RiboSeq data from BAM format alignment files", - long_description=readme + '\n\n' + history, - author="Vimalkumar Velayudhan", - author_email='vimalkumarvelayudhan@gmail.com', - url='https://github.com/vimalkumarvelayudhan/riboplot', - packages=[ - 'riboplot', - ], - package_dir={'riboplot': - 'riboplot'}, - install_requires=requirements, - license="GPL", - zip_safe=False, - keywords='riboplot', - classifiers=[ - 'Development Status :: 2 - Pre-Alpha', - 'Intended Audience :: Developers', - 'License :: OSI Approved :: GNU General Public License (GPL)', - 'Natural Language :: English', - "Programming Language :: Python :: 2", - 'Programming Language :: Python :: 2.6', - 'Programming Language :: Python :: 2.7', - ], - test_suite='tests', - tests_require=test_requirements, - entry_points={ - 'console_scripts': [ - 'riboplot = riboplot.riboplot:run', - 'ribocount = riboplot.ribocount:run'] - }, - package_data={'riboplot': ['data/*.html', 'data/css/*.gif', 'data/css/*.css', - 'data/js/*.js', 'data/js/*.map', 'scripts/*.sh']}, - exclude_package_data={'tests': ['data/*.bam', 'data/*.bai', 'data/*.fna', 'data/*.fai']} -)
--- a/tests/README.rst Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -README - test data for riboplot -=============================== -As the test data files are huge, they are not distribued with the program. - -You can download them from -http://ribogalaxy.ucc.ie/library/browse_libraries?sort=name&f-description=All&f-name=All&operation=browse&id=a799d38679e985db -
--- a/tests/data/css Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -../../data/css \ No newline at end of file
--- a/tests/data/js Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -../../data/js \ No newline at end of file
--- a/tests/data/ribocount.html Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -../../data/ribocount.html \ No newline at end of file
--- a/tests/data/ribocount_index.html Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -../../data/ribocount_index.html \ No newline at end of file
--- a/tests/data/riboplot.html Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -../../data/riboplot.html \ No newline at end of file
--- a/tests/test_ribocount.py Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ -import os -import logging -import unittest - -from riboplot import ribocore, riboplot, ribocount - -# use testing configuration -CONFIG = ribocount.CONFIG = riboplot.config.TestingConfig() -logging.disable(logging.CRITICAL) - -RIBO_FILE = os.path.join(CONFIG.TEST_DATA_DIR, '5hRPFsorted.bam') -RNA_FILE = os.path.join(CONFIG.TEST_DATA_DIR, '5hmRNAsorted.bam') -TRANSCRIPT_NAME = 'gi|148357119|ref|NM_001098396.1|' -TRANSCRIPTOME_FASTA = os.path.join(CONFIG.TEST_DATA_DIR, 'zebrafish.fna') -TRANSCRIPTOME_FASTA_MINUS1 = os.path.join(CONFIG.TEST_DATA_DIR, 'zebrafish_minus1.fna') -UNRELATED_FASTA = os.path.join(CONFIG.TEST_DATA_DIR, 'unrelated.fna') - - -class RiboCountTestCase(unittest.TestCase): - - def test_unrelated_fasta_file(self): - """If an unrelated fasta file is used, raise an error""" - parser = ribocount.create_parser() - args = parser.parse_args(['-b', RIBO_FILE, '-f', UNRELATED_FASTA]) - self.assertRaises(ribocore.ArgumentError, ribocount.main, args)
--- a/tests/test_riboplot.py Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,157 +0,0 @@ -import os -import shutil -import logging -import unittest -import tempfile - -from riboplot import ribocore, riboplot - -# use testing configuration -CONFIG = riboplot.CONFIG = riboplot.config.TestingConfig() -logging.disable(logging.CRITICAL) - -RIBO_FILE = os.path.join(CONFIG.TEST_DATA_DIR, '5hRPFsorted.bam') -RNA_FILE = os.path.join(CONFIG.TEST_DATA_DIR, '5hmRNAsorted.bam') -TRANSCRIPT_NAME = 'gi|148357119|ref|NM_001098396.1|' -TRANSCRIPTOME_FASTA = os.path.join(CONFIG.TEST_DATA_DIR, 'zebrafish.fna') -UNRELATED_BAM = os.path.join(CONFIG.TEST_DATA_DIR, 'unrelated.bam') - - -class CheckArgumentsTestCase(unittest.TestCase): - """Check if all arguments sent on the command line are valid.""" - parser = riboplot.create_parser() - - def test_bedtools_missing(self): - """If bedtools is not in PATH, raise an error.""" - args = self.parser.parse_args( - ['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-n', RNA_FILE]) - save_path = os.environ['PATH'] - os.environ['PATH'] = '' - self.assertRaises(OSError, ribocore.check_optional_arguments, ribo_file=args.ribo_file, rna_file=args.rna_file) - os.environ['PATH'] = save_path - - def test_is_bam_valid(self): - """Test if BAM file is valid.""" - valid = ribocore.is_bam_valid(RIBO_FILE) - self.assertTrue(valid) - - # test with a FASTA file (which is not BAM) - self.assertRaises(ValueError, ribocore.is_bam_valid, TRANSCRIPTOME_FASTA) - - def test_bam_has_index(self): - """Check if BAM file has an index.""" - # RPF file has an index - has_index = ribocore.bam_has_index(RIBO_FILE) - self.assertTrue(has_index) - - # RNA file doesn't have an index - has_index = ribocore.bam_has_index(RNA_FILE) - self.assertFalse(has_index) - - def test_create_bam_index(self): - """Index a BAM file.""" - ribocore.create_bam_index(RNA_FILE) - - # check if index exists - has_index = ribocore.bam_has_index(RNA_FILE) - self.assertTrue(has_index) - - # remove index - os.remove('{}.bai'.format(RNA_FILE)) - - def test_valid_read_length(self): - """Read length should be a valid integer.""" - args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, - '-t', TRANSCRIPT_NAME, '-l', '28']) - ribocore.check_optional_arguments(ribo_file=args.ribo_file, read_length=args.read_length) - - def test_invalid_read_length(self): - """An error is raised if an invalid read length is used.""" - args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, - '-l', '-1']) # invalid read length -1 - self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments, - ribo_file=args.ribo_file, read_length=args.read_length) - - args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, - '-l', '100']) # invalid read length 100 - self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments, - ribo_file=args.ribo_file, read_length=args.read_length) - - def test_valid_read_offset(self): - """Read offset should be positive.""" - args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, - '-s', '-1']) # invalid read offset -1 - self.assertRaises(ribocore.ArgumentError, ribocore.check_optional_arguments, - ribo_file=args.ribo_file, read_offset=args.read_offset) - - def test_is_fasta_valid(self): - """A valid FASTA file can be opened with pysam.FastaFile.""" - self.assertTrue(ribocore.is_fasta_valid(TRANSCRIPTOME_FASTA)) - - def test_missing_transcript_in_fasta(self): - """If a transcript is missing in FASTA, an error is raised.""" - args = self.parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME]) # invalid read offset -1 - self.assertRaises(ribocore.ArgumentError, ribocore.check_required_arguments, - args.ribo_file, args.transcriptome_fasta, 'hello') - - def test_missing_transcript_in_bam(self): - """If a transcript is missing in BAM, an error is raised.""" - # testing with an unrelated BAM file - args = self.parser.parse_args(['-b', UNRELATED_BAM, '-f', TRANSCRIPTOME_FASTA, - '-t', TRANSCRIPT_NAME]) - self.assertRaises(ribocore.ArgumentError, ribocore.check_required_arguments, args.ribo_file, - args.transcriptome_fasta, args.transcript_name) - - -class RNACountsTestCase(unittest.TestCase): - - def test_get_rna_counts(self): - """Test get RNA counts for transcript from RNA-Seq BAM file. Assumes bedtools is installed.""" - counts = riboplot.get_rna_counts(RNA_FILE, TRANSCRIPT_NAME) - self.assertIsInstance(counts, dict) - self.assertTrue(len(counts) > 0) - - def test_invalid_rna_file(self): - """If an invalid RNA file is provided, generate an error message""" - # using transcriptome FASTA file as the invalid RNA file for test - parser = riboplot.create_parser() - args = parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, '-n', TRANSCRIPTOME_FASTA]) - self.assertRaises(ValueError, ribocore.check_optional_arguments, ribo_file=args.ribo_file, rna_file=args.rna_file) - - -class RiboPlotTestCase(unittest.TestCase): - - def test_get_codon_positions(self): - """Get codon positions in all frames given a sequence.""" - # the positions on this sequence were calculated manually. - fasta = ('AACCGGAGCACCCAGAGAAAACCCACGCAAACGCAGGGAGAATTTGCAAACTCCACACA' - 'GAAATGCCAGCTGATCCAGCCGAGCCTCGAGTCAGCATCCTTGCTTGTTGGATGCCTGA' - 'TTGCAGTTCAACTCCAAACTCAGTTGGACCAGCTGATCAGTG') - codon_positions = riboplot.get_start_stops(fasta) - expected = {1: {'starts': [], 'stops': []}, - 2: {'starts': [], 'stops': [71, 116, 152]}, - 3: {'starts': [63, 111], 'stops': []}} - self.assertEqual(codon_positions, expected) - - def test_valid_riboplot_run(self): - """A good riboplot run""" - output_dir = tempfile.mkdtemp() - print 'Output path is {}'.format(output_dir) - parser = riboplot.create_parser() - args = parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', TRANSCRIPT_NAME, - '-o', output_dir]) - riboplot.main(args) - for fname in ('riboplot.png', 'riboplot.svg', 'RiboCounts.csv'): - self.assertTrue(os.path.exists(os.path.join(output_dir, fname))) - shutil.rmtree(output_dir) - - def test_transcript_with_no_counts(self): - """If the transcript has no ribocounts, no plot should be produced.""" - transcript = 'gi|62955616|ref|NM_001017822.1|' # has no reads - output_dir = tempfile.mkdtemp() - parser = riboplot.create_parser() - args = parser.parse_args(['-b', RIBO_FILE, '-f', TRANSCRIPTOME_FASTA, '-t', transcript, '-o', output_dir]) - self.assertRaises(ribocore.RiboPlotError, riboplot.main, args) - for fname in ('riboplot.png', 'riboplot.svg', 'RiboCounts.csv'): - self.assertFalse(os.path.exists(os.path.join(output_dir, fname))) - shutil.rmtree(output_dir)
--- a/tool_dependencies.xml Mon Aug 31 11:41:48 2015 +0100 +++ b/tool_dependencies.xml Mon Aug 31 14:13:03 2015 +0100 @@ -1,13 +1,29 @@ <?xml version="1.0"?> <tool_dependency> - <package name="matplotlib" version="1.2.1"> - <repository changeset_revision="50b86df1f968" name="package_matplotlib_1_2" - owner="iuc" prior_installation_required="True" - /> + <package name="ez_setup" version="0.9"> + <repository changeset_revision="f50b27b88d30" name="package_ez_setup_0_9" owner="iuc" + prior_installation_required="True"/> </package> - <package name="pysam" version="0.8.3"> - <repository changeset_revision="ee642ed79a3b" name="package_python_2_7_pysam_0_8_3" - owner="iuc" prior_installation_required="True" - /> + <package name="riboplot" version="0.1.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://pypi.python.org/packages/source/r/riboplot/riboplot-0.1.0.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="f50b27b88d30" name="package_ez_setup_0_9" owner="iuc"> + <package name="ez_setup" version="0.9" /> + </repository> + </action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="set_to" name="RIBOPLOT_PATH">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + Requires installation of matplotlib 1.3.1 and pysam 0.8.3. RNA coverage requires bedtools installed. + </readme> </package> </tool_dependency>
--- a/tox.ini Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -[tox] -envlist = py26, py27, py33, py34 - -[testenv] -setenv = - PYTHONPATH = {toxinidir}:{toxinidir}/riboplot -commands = python setup.py test -deps = - -r{toxinidir}/requirements.txt \ No newline at end of file