# HG changeset patch # User Vimalkumar Velayudhan # Date 1441026783 -3600 # Node ID cff63cf0dea839cb375a41a4816fef352df6cced # Parent 805b779d4013979147c631ee315d31aefe6cf7a5 Update tool_dependencies to install package from pip diff -r 805b779d4013 -r cff63cf0dea8 AUTHORS.rst --- 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 - -Contributors ------------- - -None yet. Why not be the first? \ No newline at end of file diff -r 805b779d4013 -r cff63cf0dea8 CONTRIBUTING.rst --- 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 diff -r 805b779d4013 -r cff63cf0dea8 HISTORY.rst --- 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. diff -r 805b779d4013 -r cff63cf0dea8 LICENSE --- 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 diff -r 805b779d4013 -r cff63cf0dea8 MANIFEST.in --- 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 diff -r 805b779d4013 -r cff63cf0dea8 Makefile --- 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 - $(MAKE) -C docs html - -release: clean - python setup.py sdist upload - python setup.py bdist_wheel upload - -dist: clean - python setup.py sdist - python setup.py bdist_wheel - ls -l dist - -install: clean - python setup.py install diff -r 805b779d4013 -r cff63cf0dea8 README.rst --- a/README.rst Mon Aug 31 11:41:48 2015 +0100 +++ b/README.rst Mon Aug 31 14:13:03 2015 +0100 @@ -1,6 +1,6 @@ -=============================== +======== RiboPlot -=============================== +======== .. image:: https://img.shields.io/travis/vimalkumarvelayudhan/riboplot.svg :target: https://travis-ci.org/vimalkumarvelayudhan/riboplot @@ -14,13 +14,39 @@ There are two programs in the package: **riboplot** + Plot and output read counts (csv) for a single transcript. **ribocount** + Output read counts for all transcripts in an alignment. +Free software: GPL license -Free software: GPL license. +Documentation: https://riboplot.readthedocs.org + +Repository: https://github.com/vimalkumarvelayudhan/riboplot + +Requirements +------------ +Python packages +............... +* matplotlib ``1.3.1`` +* pysam ``0.8.3`` -Documentation: https://riboplot.readthedocs.org. +If you have a virtualenv setup, these packages and their dependencies can be installed +using:: + + pip install matplotlib==1.3.1 + pip install pysam==0.8.3 +Bedtools +........ +RNA coverage plot requires `bedtools `_ to be installed. + +This release of riboplot has been tested with bedtools version ``2.17.0``. + +On Ubuntu and derivatives, bedtools can be installed from the repositories using:: + + sudo apt-get install bedtools + diff -r 805b779d4013 -r cff63cf0dea8 docs/Makefile --- a/docs/Makefile Mon Aug 31 11:41:48 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,177 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -PAPER = -BUILDDIR = _build - -# User-friendly check for sphinx-build -ifeq ($(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 ' where 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. The message catalogs are in $(BUILDDIR)/locale." - -changes: - $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes - @echo - @echo "The overview file is in $(BUILDDIR)/changes." - -linkcheck: - $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck - @echo - @echo "Link check complete; look for any errors in the above output " \ - "or in $(BUILDDIR)/linkcheck/output.txt." - -doctest: - $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest - @echo "Testing of doctests in the sources finished, look at the " \ - "results in $(BUILDDIR)/doctest/output.txt." - -xml: - $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml - @echo - @echo "Build finished. The XML files are in $(BUILDDIR)/xml." - -pseudoxml: - $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml - @echo - @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." \ No newline at end of file diff -r 805b779d4013 -r cff63cf0dea8 docs/_static/alabaster.css_t --- 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; -} - -div.sphinxsidebar p { - color: {{ theme_sidebar_text }}; - margin: 10px 0; -} - -div.sphinxsidebar ul { - margin: 10px 0; - padding: 0; - color: {{ theme_sidebar_list }}; -} - -div.sphinxsidebar ul li.toctree-l1 > a { - font-size: 120%; -} - -div.sphinxsidebar ul li.toctree-l2 > a { - font-size: 110%; -} - -div.sphinxsidebar input { - border: 1px solid {{ theme_sidebar_search_button }}; - font-family: {{ theme_font_family }}; - font-size: 1.1em; -} - -div.sphinxsidebar hr { - border: none; - height: 1px; - color: {{ theme_sidebar_link_underscore }}; - background: {{ theme_sidebar_link_underscore }}; - - text-align: left; - margin-left: 0; - width: 50%; -} - -/* -- body styles ----------------------------------------------------------- */ - -a { - color: {{ theme_link }}; - text-decoration: underline; -} - -a:hover { - color: {{ theme_link_hover }}; - text-decoration: underline; -} - -div.body h1, -div.body h2, -div.body h3, -div.body h4, -div.body h5, -div.body h6 { - font-family: {{ theme_head_font_family }}; - 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; -} diff -r 805b779d4013 -r cff63cf0dea8 docs/_static/riboplot-logo.png Binary file docs/_static/riboplot-logo.png has changed diff -r 805b779d4013 -r cff63cf0dea8 docs/_styles/custom.style --- 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 diff -r 805b779d4013 -r cff63cf0dea8 docs/_styles/fonts/Cabin-Bold.ttf Binary file docs/_styles/fonts/Cabin-Bold.ttf has changed diff -r 805b779d4013 -r cff63cf0dea8 docs/_styles/fonts/Cabin-BoldItalic.ttf Binary file docs/_styles/fonts/Cabin-BoldItalic.ttf has changed diff -r 805b779d4013 -r cff63cf0dea8 docs/_styles/fonts/Cabin-Italic.ttf Binary file docs/_styles/fonts/Cabin-Italic.ttf has changed diff -r 805b779d4013 -r cff63cf0dea8 docs/_styles/fonts/Cabin-Regular.ttf Binary file docs/_styles/fonts/Cabin-Regular.ttf has changed diff -r 805b779d4013 -r cff63cf0dea8 docs/_styles/fonts/SourceSansPro-Bold.ttf Binary file docs/_styles/fonts/SourceSansPro-Bold.ttf has changed diff -r 805b779d4013 -r cff63cf0dea8 docs/_styles/fonts/SourceSansPro-BoldItalic.ttf Binary file docs/_styles/fonts/SourceSansPro-BoldItalic.ttf has changed diff -r 805b779d4013 -r cff63cf0dea8 docs/_styles/fonts/SourceSansPro-Italic.ttf Binary file docs/_styles/fonts/SourceSansPro-Italic.ttf has changed diff -r 805b779d4013 -r cff63cf0dea8 docs/_styles/fonts/SourceSansPro-Regular.ttf Binary file docs/_styles/fonts/SourceSansPro-Regular.ttf has changed diff -r 805b779d4013 -r cff63cf0dea8 docs/_templates/about.html --- 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 @@ -

{{ project }}

diff -r 805b779d4013 -r cff63cf0dea8 docs/_templates/layout.html --- 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 %} - - {% endif %} - -{% endblock %} -{%- block relbar2 %}{% endblock %} -{%- block footer %} -
- - {%- if last_updated %} - {% trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %} - {%- endif %} - - - {% if theme_show_powered_by|lower == 'true' %} - | - Powered by Sphinx {{ sphinx_version }} - & Alabaster {{ alabaster_version }} - {% endif %} - {%- if show_source and has_source and sourcename %} - | - {{ _('Page source') }} - {%- endif %} -
- - {% if theme_github_banner|lower != 'false' %} - - Fork me on GitHub - - {% endif %} - - {% if theme_analytics_id %} - - {% endif %} -{%- endblock %} diff -r 805b779d4013 -r cff63cf0dea8 docs/_templates/searchbox.html --- 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" %} - - -{%- endif %} diff -r 805b779d4013 -r cff63cf0dea8 docs/authors.rst --- 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 diff -r 805b779d4013 -r cff63cf0dea8 docs/conf.py --- 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 -# " v 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 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 diff -r 805b779d4013 -r cff63cf0dea8 docs/contributing.rst --- 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 diff -r 805b779d4013 -r cff63cf0dea8 docs/history.rst --- 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 diff -r 805b779d4013 -r cff63cf0dea8 docs/index.rst --- 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` diff -r 805b779d4013 -r cff63cf0dea8 docs/installation.rst --- 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 `_ 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 diff -r 805b779d4013 -r cff63cf0dea8 docs/make.bat --- 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 ^` where ^ 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. The HTML pages are in %BUILDDIR%/singlehtml. - goto end -) - -if "%1" == "pickle" ( - %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can process the pickle files. - goto end -) - -if "%1" == "json" ( - %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can process the JSON files. - goto end -) - -if "%1" == "htmlhelp" ( - %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can run HTML Help Workshop with the ^ -.hhp project file in %BUILDDIR%/htmlhelp. - goto end -) - -if "%1" == "qthelp" ( - %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp - if errorlevel 1 exit /b 1 - 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.ghc - goto end -) - -if "%1" == "devhelp" ( - %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. - goto end -) - -if "%1" == "epub" ( - %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The epub file is in %BUILDDIR%/epub. - goto end -) - -if "%1" == "latex" ( - %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. - goto end -) - -if "%1" == "latexpdf" ( - %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex - cd %BUILDDIR%/latex - make all-pdf - cd %BUILDDIR%/.. - echo. - echo.Build finished; the PDF files are in %BUILDDIR%/latex. - goto end -) - -if "%1" == "latexpdfja" ( - %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex - cd %BUILDDIR%/latex - make all-pdf-ja - cd %BUILDDIR%/.. - echo. - echo.Build finished; the PDF files are in %BUILDDIR%/latex. - goto end -) - -if "%1" == "text" ( - %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The text files are in %BUILDDIR%/text. - goto end -) - -if "%1" == "man" ( - %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The manual pages are in %BUILDDIR%/man. - goto end -) - -if "%1" == "texinfo" ( - %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. - goto end -) - -if "%1" == "gettext" ( - %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The message catalogs are in %BUILDDIR%/locale. - goto end -) - -if "%1" == "changes" ( - %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes - if errorlevel 1 exit /b 1 - echo. - echo.The overview file is in %BUILDDIR%/changes. - goto end -) - -if "%1" == "linkcheck" ( - %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck - if errorlevel 1 exit /b 1 - echo. - echo.Link check complete; look for any errors in the above output ^ -or in %BUILDDIR%/linkcheck/output.txt. - goto end -) - -if "%1" == "doctest" ( - %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest - if errorlevel 1 exit /b 1 - echo. - echo.Testing of doctests in the sources finished, look at the ^ -results in %BUILDDIR%/doctest/output.txt. - goto end -) - -if "%1" == "xml" ( - %SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. 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 diff -r 805b779d4013 -r cff63cf0dea8 docs/readme.rst --- 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 diff -r 805b779d4013 -r cff63cf0dea8 docs/todo.rst --- 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. - - diff -r 805b779d4013 -r cff63cf0dea8 docs/usage.rst --- 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 - diff -r 805b779d4013 -r cff63cf0dea8 images/ribocount.png Binary file images/ribocount.png has changed diff -r 805b779d4013 -r cff63cf0dea8 images/riboplot.png Binary file images/riboplot.png has changed diff -r 805b779d4013 -r cff63cf0dea8 ribocount.xml --- 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 @@ Get read counts for all transcripts in an alignment (BAM) - pysam + riboplot - riboplot/ribocount.py + ribocount --ribo_file "${ribo_file}" --transcriptome_fasta "${transcriptome_fasta}" --read_length "${read_length}" diff -r 805b779d4013 -r cff63cf0dea8 riboplot.egg-info/PKG-INFO --- 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 diff -r 805b779d4013 -r cff63cf0dea8 riboplot.egg-info/SOURCES.txt --- 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 diff -r 805b779d4013 -r cff63cf0dea8 riboplot.egg-info/dependency_links.txt --- 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 @@ - diff -r 805b779d4013 -r cff63cf0dea8 riboplot.egg-info/entry_points.txt --- 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 - diff -r 805b779d4013 -r cff63cf0dea8 riboplot.egg-info/not-zip-safe --- 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 @@ - diff -r 805b779d4013 -r cff63cf0dea8 riboplot.egg-info/requires.txt --- 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 diff -r 805b779d4013 -r cff63cf0dea8 riboplot.egg-info/top_level.txt --- 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 diff -r 805b779d4013 -r cff63cf0dea8 riboplot.xml --- 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 @@ Plot and output read counts for a single transcript in an alignment (BAM) - matplotlib - pysam + riboplot - riboplot/riboplot.py + riboplot --ribo_file "${ribo_file}" --transcriptome_fasta "${transcriptome_fasta}" --transcript_name "${transcript_name}" diff -r 805b779d4013 -r cff63cf0dea8 riboplot/__init__.py --- 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' diff -r 805b779d4013 -r cff63cf0dea8 riboplot/config.py --- 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 diff -r 805b779d4013 -r cff63cf0dea8 riboplot/data/css/asc.gif Binary file riboplot/data/css/asc.gif has changed diff -r 805b779d4013 -r cff63cf0dea8 riboplot/data/css/bg.gif Binary file riboplot/data/css/bg.gif has changed diff -r 805b779d4013 -r cff63cf0dea8 riboplot/data/css/custom.css --- 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 diff -r 805b779d4013 -r cff63cf0dea8 riboplot/data/css/desc.gif Binary file riboplot/data/css/desc.gif has changed diff -r 805b779d4013 -r cff63cf0dea8 riboplot/data/css/normalize.css --- 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 diff -r 805b779d4013 -r cff63cf0dea8 riboplot/data/css/skeleton.css --- 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) {} diff -r 805b779d4013 -r cff63cf0dea8 riboplot/data/js/custom.js --- 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(); - }); -} -); diff -r 805b779d4013 -r cff63cf0dea8 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