| Previous changeset 13:8a87a2c44d09 (2015-08-21) Next changeset 15:b78a5ba760b1 (2015-08-27) |
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Commit message:
Version as released on PyPI 0.1.0 |
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modified:
AUTHORS.rst CONTRIBUTING.rst HISTORY.rst MANIFEST.in README.rst docs/_static/alabaster.css_t docs/authors.rst docs/conf.py docs/contributing.rst docs/history.rst docs/index.rst docs/installation.rst docs/readme.rst docs/riboplot.rst docs/todo.rst docs/usage.rst requirements.txt riboplot.egg-info/PKG-INFO riboplot.egg-info/SOURCES.txt riboplot/config.py riboplot/ribocount.py riboplot/riboplot.py setup.py tests/test_ribocount.py tests/test_riboplot.py |
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.editorconfig docs/_static/riboplot-logo.png riboplot.egg-info/entry_points.txt riboplot.egg-info/requires.txt 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/scripts/run_coverage.sh riboplot/scripts/run_ribocount_sample.sh riboplot/scripts/run_riboplot_sample.sh riboplot/scripts/run_tests.sh tests/README.rst |
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removed:
data/css/asc.gif data/css/bg.gif data/css/custom.css data/css/desc.gif data/css/normalize.css data/css/skeleton.css data/js/custom.js data/js/jquery-1.11.3.min.js data/js/jquery-1.11.3.min.map data/js/jquery.tablesorter.min.js data/ribocount.html data/ribocount_index.html data/riboplot.html run_coverage.sh run_ribocount_sample.sh run_riboplot_sample.sh run_tests.sh |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 .editorconfig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.editorconfig Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -0,0 +1,21 @@ +# http://editorconfig.org + +root = true + +[*] +indent_style = space +indent_size = 4 +trim_trailing_whitespace = true +insert_final_newline = true +charset = utf-8 +end_of_line = lf + +[*.bat] +indent_style = tab +end_of_line = crlf + +[LICENSE] +insert_final_newline = false + +[Makefile] +indent_style = tab \ No newline at end of file |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 AUTHORS.rst --- a/AUTHORS.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/AUTHORS.rst Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -1,1 +1,13 @@ -docs/authors.rst \ No newline at end of file +======= +Credits +======= + +Development Lead +---------------- + +* Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> + +Contributors +------------ + +None yet. Why not be the first? \ No newline at end of file |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 CONTRIBUTING.rst --- a/CONTRIBUTING.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/CONTRIBUTING.rst Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -1,1 +1,111 @@ -docs/contributing.rst \ No newline at end of file +============ +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 |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 HISTORY.rst --- a/HISTORY.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/HISTORY.rst Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -1,1 +1,9 @@ -docs/history.rst \ No newline at end of file +.. :changelog: + +History +======= + +0.1.0 (2015-08-24) +--------------------- + +* First release on PyPI. |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 MANIFEST.in --- a/MANIFEST.in Fri Aug 21 12:37:54 2015 +0100 +++ b/MANIFEST.in Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -1,11 +1,2 @@ -include AUTHORS.rst -include CONTRIBUTING.rst -include HISTORY.rst -include LICENSE -include README.rst - -recursive-include tests * -recursive-exclude * __pycache__ recursive-exclude * *.py[co] - -recursive-include docs *.rst conf.py Makefile make.bat \ No newline at end of file +exclude riboplot/riboplot_multi.py |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 README.rst --- a/README.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/README.rst Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -1,1 +1,28 @@ -docs/readme.rst \ No newline at end of file +=============================== +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. + |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 data/css/custom.css --- a/data/css/custom.css Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 data/css/normalize.css --- a/data/css/normalize.css Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,427 +0,0 @@\n-/*! normalize.css v3.0.2 | MIT License | git.io/normalize */\n-\n-/**\n- * 1. Set default font family to sans-serif.\n- * 2. Prevent iOS text size adjust after orientation change, without disabling\n- * user zoom.\n- */\n-\n-html {\n- font-family: sans-serif; /* 1 */\n- -ms-text-size-adjust: 100%; /* 2 */\n- -webkit-text-size-adjust: 100%; /* 2 */\n-}\n-\n-/**\n- * Remove default margin.\n- */\n-\n-body {\n- margin: 0;\n-}\n-\n-/* HTML5 display definitions\n- ========================================================================== */\n-\n-/**\n- * Correct `block` display not defined for any HTML5 element in IE 8/9.\n- * Correct `block` display not defined for `details` or `summary` in IE 10/11\n- * and Firefox.\n- * Correct `block` display not defined for `main` in IE 11.\n- */\n-\n-article,\n-aside,\n-details,\n-figcaption,\n-figure,\n-footer,\n-header,\n-hgroup,\n-main,\n-menu,\n-nav,\n-section,\n-summary {\n- display: block;\n-}\n-\n-/**\n- * 1. Correct `inline-block` display not defined in IE 8/9.\n- * 2. Normalize vertical alignment of `progress` in Chrome, Firefox, and Opera.\n- */\n-\n-audio,\n-canvas,\n-progress,\n-video {\n- display: inline-block; /* 1 */\n- vertical-align: baseline; /* 2 */\n-}\n-\n-/**\n- * Prevent modern browsers from displaying `audio` without controls.\n- * Remove excess height in iOS 5 devices.\n- */\n-\n-audio:not([controls]) {\n- display: none;\n- height: 0;\n-}\n-\n-/**\n- * Address `[hidden]` styling not present in IE 8/9/10.\n- * Hide the `template` element in IE 8/9/11, Safari, and Firefox < 22.\n- */\n-\n-[hidden],\n-template {\n- display: none;\n-}\n-\n-/* Links\n- ========================================================================== */\n-\n-/**\n- * Remove the gray background color from active links in IE 10.\n- */\n-\n-a {\n- background-color: transparent;\n-}\n-\n-/**\n- * Improve readability when focused and also mouse hovered in all browsers.\n- */\n-\n-a:active,\n-a:hover {\n- outline: 0;\n-}\n-\n-/* Text-level semantics\n- ========================================================================== */\n-\n-/**\n- * Address styling not present in IE 8/9/10/11, Safari, and Chrome.\n- */\n-\n-abbr[title] {\n- border-bottom: 1px dotted;\n-}\n-\n-/**\n- * Address style set to `bolder` in Firefox 4+, Safari, and Chrome.\n- */\n-\n-b,\n-strong {\n- font-weight: bold;\n-}\n-\n-/**\n- * Address styling not present in Safari and Chrome.\n- */\n-\n-dfn {\n- font-style: italic;\n-}\n-\n-/**\n- * Address variable `h1` font-size and margin within `section` and `article`\n- * contexts in Firefox 4+, Safari, and Chrome.\n- */\n-\n-h1 {\n- font-size: 2em;\n- margin: 0.67em 0;\n-}\n-\n-/**\n- * Address styling not present in IE 8/9.\n- */\n-\n-mark {\n- background: #ff0;\n- color: #000;\n-}\n-\n-/**\n- * Address inconsistent and variable font size in all browsers.\n- */\n-\n-small {\n- font-size: 80%;\n-}\n-\n-/**\n- * Prevent `sub` and `sup` affecting `line-height` in all browsers.\n- */\n-\n-sub,\n-sup {\n- font-size: 75%;\n- line-height: 0;\n- position: relative;\n- vertical-align: baseline;\n-}\n-\n-sup {\n- top: -0.5em;\n-}\n-\n-sub {\n- bottom: -0.25em;\n-}\n-\n-/* Embedded content\n- ========================================================================== */\n-\n-/**\n- * Remove border when inside `a` element in IE 8/9/10.\n- */\n-\n-img {\n- border: 0;\n-}\n-\n-/**\n- * Correct overflow not hidden in IE 9/10/11.\n- */\n-\n-svg:not(:root) {\n- overflow: hidden;\n-}\n-\n-/* Grouping content\n- ========================================================================== */\n-\n-/**\n- * Address margin not present in IE 8/9 and Safari.\n- */\n-\n-figure {\n- margin: 1em 40px;\n-}\n-\n-/**\n- * Address differences between Firefox and other browsers.\n- */\n-\n-hr {\n- -moz-box-sizing: content-box;\n- box-sizing: content-box;\n- height: 0;\n-}\n-\n-/**\n- * Contain overflow in all browsers.\n- */\n-\n-pre {\n- overflow: auto;\n-}\n-\n-/**\n- * Address odd `em`-unit font size rendering in all browsers.\n- */\n-\n-code,\n-kbd,\n-pre,\n-samp {\n- font-family: monospace, monospace;\n- font-size: 1em;\n-}\n-\n-/* Forms\n- ======================================'..b' of disabled elements.\n- * 2. Correct font properties not being inherited.\n- * 3. Address margins set differently in Firefox 4+, Safari, and Chrome.\n- */\n-\n-button,\n-input,\n-optgroup,\n-select,\n-textarea {\n- color: inherit; /* 1 */\n- font: inherit; /* 2 */\n- margin: 0; /* 3 */\n-}\n-\n-/**\n- * Address `overflow` set to `hidden` in IE 8/9/10/11.\n- */\n-\n-button {\n- overflow: visible;\n-}\n-\n-/**\n- * Address inconsistent `text-transform` inheritance for `button` and `select`.\n- * All other form control elements do not inherit `text-transform` values.\n- * Correct `button` style inheritance in Firefox, IE 8/9/10/11, and Opera.\n- * Correct `select` style inheritance in Firefox.\n- */\n-\n-button,\n-select {\n- text-transform: none;\n-}\n-\n-/**\n- * 1. Avoid the WebKit bug in Android 4.0.* where (2) destroys native `audio`\n- * and `video` controls.\n- * 2. Correct inability to style clickable `input` types in iOS.\n- * 3. Improve usability and consistency of cursor style between image-type\n- * `input` and others.\n- */\n-\n-button,\n-html input[type="button"], /* 1 */\n-input[type="reset"],\n-input[type="submit"] {\n- -webkit-appearance: button; /* 2 */\n- cursor: pointer; /* 3 */\n-}\n-\n-/**\n- * Re-set default cursor for disabled elements.\n- */\n-\n-button[disabled],\n-html input[disabled] {\n- cursor: default;\n-}\n-\n-/**\n- * Remove inner padding and border in Firefox 4+.\n- */\n-\n-button::-moz-focus-inner,\n-input::-moz-focus-inner {\n- border: 0;\n- padding: 0;\n-}\n-\n-/**\n- * Address Firefox 4+ setting `line-height` on `input` using `!important` in\n- * the UA stylesheet.\n- */\n-\n-input {\n- line-height: normal;\n-}\n-\n-/**\n- * It\'s recommended that you don\'t attempt to style these elements.\n- * Firefox\'s implementation doesn\'t respect box-sizing, padding, or width.\n- *\n- * 1. Address box sizing set to `content-box` in IE 8/9/10.\n- * 2. Remove excess padding in IE 8/9/10.\n- */\n-\n-input[type="checkbox"],\n-input[type="radio"] {\n- box-sizing: border-box; /* 1 */\n- padding: 0; /* 2 */\n-}\n-\n-/**\n- * Fix the cursor style for Chrome\'s increment/decrement buttons. For certain\n- * `font-size` values of the `input`, it causes the cursor style of the\n- * decrement button to change from `default` to `text`.\n- */\n-\n-input[type="number"]::-webkit-inner-spin-button,\n-input[type="number"]::-webkit-outer-spin-button {\n- height: auto;\n-}\n-\n-/**\n- * 1. Address `appearance` set to `searchfield` in Safari and Chrome.\n- * 2. Address `box-sizing` set to `border-box` in Safari and Chrome\n- * (include `-moz` to future-proof).\n- */\n-\n-input[type="search"] {\n- -webkit-appearance: textfield; /* 1 */\n- -moz-box-sizing: content-box;\n- -webkit-box-sizing: content-box; /* 2 */\n- box-sizing: content-box;\n-}\n-\n-/**\n- * Remove inner padding and search cancel button in Safari and Chrome on OS X.\n- * Safari (but not Chrome) clips the cancel button when the search input has\n- * padding (and `textfield` appearance).\n- */\n-\n-input[type="search"]::-webkit-search-cancel-button,\n-input[type="search"]::-webkit-search-decoration {\n- -webkit-appearance: none;\n-}\n-\n-/**\n- * Define consistent border, margin, and padding.\n- */\n-\n-fieldset {\n- border: 1px solid #c0c0c0;\n- margin: 0 2px;\n- padding: 0.35em 0.625em 0.75em;\n-}\n-\n-/**\n- * 1. Correct `color` not being inherited in IE 8/9/10/11.\n- * 2. Remove padding so people aren\'t caught out if they zero out fieldsets.\n- */\n-\n-legend {\n- border: 0; /* 1 */\n- padding: 0; /* 2 */\n-}\n-\n-/**\n- * Remove default vertical scrollbar in IE 8/9/10/11.\n- */\n-\n-textarea {\n- overflow: auto;\n-}\n-\n-/**\n- * Don\'t inherit the `font-weight` (applied by a rule above).\n- * NOTE: the default cannot safely be changed in Chrome and Safari on OS X.\n- */\n-\n-optgroup {\n- font-weight: bold;\n-}\n-\n-/* Tables\n- ========================================================================== */\n-\n-/**\n- * Remove most spacing between table cells.\n- */\n-\n-table {\n- border-collapse: collapse;\n- border-spacing: 0;\n-}\n-\n-td,\n-th {\n- padding: 0;\n-}\n\\ No newline at end of file\n' |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 data/css/skeleton.css --- a/data/css/skeleton.css Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,419 +0,0 @@\n-/*\n-* Skeleton V2.0.4\n-* Copyright 2014, Dave Gamache\n-* www.getskeleton.com\n-* Free to use under the MIT license.\n-* http://www.opensource.org/licenses/mit-license.php\n-* 12/29/2014\n-*/\n-\n-\n-/* Table of contents\n-\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\n-- Grid\n-- Base Styles\n-- Typography\n-- Links\n-- Buttons\n-- Forms\n-- Lists\n-- Code\n-- Tables\n-- Spacing\n-- Utilities\n-- Clearing\n-- Media Queries\n-*/\n-\n-\n-/* Grid\n-\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n-.container {\n- position: relative;\n- width: 100%;\n- max-width: 960px;\n- margin: 0 auto;\n- padding: 0 20px;\n- box-sizing: border-box; }\n-.column,\n-.columns {\n- width: 100%;\n- float: left;\n- box-sizing: border-box; }\n-\n-/* For devices larger than 400px */\n-@media (min-width: 400px) {\n- .container {\n- width: 85%;\n- padding: 0; }\n-}\n-\n-/* For devices larger than 550px */\n-@media (min-width: 550px) {\n- .container {\n- width: 80%; }\n- .column,\n- .columns {\n- margin-left: 4%; }\n- .column:first-child,\n- .columns:first-child {\n- margin-left: 0; }\n-\n- .one.column,\n- .one.columns { width: 4.66666666667%; }\n- .two.columns { width: 13.3333333333%; }\n- .three.columns { width: 22%; }\n- .four.columns { width: 30.6666666667%; }\n- .five.columns { width: 39.3333333333%; }\n- .six.columns { width: 48%; }\n- .seven.columns { width: 56.6666666667%; }\n- .eight.columns { width: 65.3333333333%; }\n- .nine.columns { width: 74.0%; }\n- .ten.columns { width: 82.6666666667%; }\n- .eleven.columns { width: 91.3333333333%; }\n- .twelve.columns { width: 100%; margin-left: 0; }\n-\n- .one-third.column { width: 30.6666666667%; }\n- .two-thirds.column { width: 65.3333333333%; }\n-\n- .one-half.column { width: 48%; }\n-\n- /* Offsets */\n- .offset-by-one.column,\n- .offset-by-one.columns { margin-left: 8.66666666667%; }\n- .offset-by-two.column,\n- .offset-by-two.columns { margin-left: 17.3333333333%; }\n- .offset-by-three.column,\n- .offset-by-three.columns { margin-left: 26%; }\n- .offset-by-four.column,\n- .offset-by-four.columns { margin-left: 34.6666666667%; }\n- .offset-by-five.column,\n- .offset-by-five.columns { margin-left: 43.3333333333%; }\n- .offset-by-six.column,\n- .offset-by-six.columns { margin-left: 52%; }\n- .offset-by-seven.column,\n- .offset-by-seven.columns { margin-left: 60.6666666667%; }\n- .offset-by-eight.column,\n- .offset-by-eight.columns { margin-left: 69.3333333333%; }\n- .offset-by-nine.column,\n- .offset-by-nine.columns { margin-left: 78.0%; }\n- .offset-by-ten.column,\n- .offset-by-ten.columns { margin-left: 86.6666666667%; }\n- .offset-by-eleven.column,\n- .offset-by-eleven.columns { margin-left: 95.3333333333%; }\n-\n- .offset-by-one-third.column,\n- .offset-by-one-third.columns { margin-left: 34.6666666667%; }\n- .offset-by-two-thirds.column,\n- .offset-by-two-thirds.columns { margin-left: 69.3333333333%; }\n-\n- .offset-by-one-half.column,\n- .offset-by-one-half.columns { margin-left: 52%; }\n-\n-}\n-\n-\n-/* Base Styles\n-\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n-/* NOTE\n-html is set to 62.5% so that all the REM measurements throughout Skeleton\n-are based on 10px sizing. So basically 1.5rem = 15px :) */\n-html {\n- font-size: 62.5%; }\n-body {\n- font-size: 1.5em; /* currently ems cause chrome bug '..b'none; }\n-textarea {\n- min-height: 65px;\n- padding-top: 6px;\n- padding-bottom: 6px; }\n-input[type="email"]:focus,\n-input[type="number"]:focus,\n-input[type="search"]:focus,\n-input[type="text"]:focus,\n-input[type="tel"]:focus,\n-input[type="url"]:focus,\n-input[type="password"]:focus,\n-textarea:focus,\n-select:focus {\n- border: 1px solid #33C3F0;\n- outline: 0; }\n-label,\n-legend {\n- display: block;\n- margin-bottom: .5rem;\n- font-weight: 600; }\n-fieldset {\n- padding: 0;\n- border-width: 0; }\n-input[type="checkbox"],\n-input[type="radio"] {\n- display: inline; }\n-label > .label-body {\n- display: inline-block;\n- margin-left: .5rem;\n- font-weight: normal; }\n-\n-\n-/* Lists\n-\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n-ul {\n- list-style: circle inside; }\n-ol {\n- list-style: decimal inside; }\n-ol, ul {\n- padding-left: 0;\n- margin-top: 0; }\n-ul ul,\n-ul ol,\n-ol ol,\n-ol ul {\n- margin: 1.5rem 0 1.5rem 3rem;\n- font-size: 90%; }\n-li {\n- margin-bottom: 1rem; }\n-\n-\n-/* Code\n-\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n-code {\n- padding: .2rem .5rem;\n- margin: 0 .2rem;\n- font-size: 90%;\n- white-space: nowrap;\n- background: #F1F1F1;\n- border: 1px solid #E1E1E1;\n- border-radius: 4px; }\n-pre > code {\n- display: block;\n- padding: 1rem 1.5rem;\n- white-space: pre; }\n-\n-\n-/* Tables\n-\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n-th,\n-td {\n- padding: 12px 15px;\n- text-align: left;\n- border-bottom: 1px solid #E1E1E1; }\n-\n-/*th:first-child,\n-td:first-child {\n- padding-left: 0; }\n-th:last-child,\n-td:last-child {\n- padding-right: 0; }\n-*/\n-\n-/* Spacing\n-\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n-button,\n-.button {\n- margin-bottom: 1rem; }\n-input,\n-textarea,\n-select,\n-fieldset {\n- margin-bottom: 1.5rem; }\n-pre,\n-blockquote,\n-dl,\n-figure,\n-table,\n-p,\n-ul,\n-ol,\n-form {\n- margin-bottom: 2.5rem; }\n-\n-\n-/* Utilities\n-\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n-.u-full-width {\n- width: 100%;\n- box-sizing: border-box; }\n-.u-max-full-width {\n- max-width: 100%;\n- box-sizing: border-box; }\n-.u-pull-right {\n- float: right; }\n-.u-pull-left {\n- float: left; }\n-\n-\n-/* Misc\n-\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n-hr {\n- margin-top: 3rem;\n- margin-bottom: 3.5rem;\n- border-width: 0;\n- border-top: 1px solid #E1E1E1; }\n-\n-\n-/* Clearing\n-\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n-\n-/* Self Clearing Goodness */\n-.container:after,\n-.row:after,\n-.u-cf {\n- content: "";\n- display: table;\n- clear: both; }\n-\n-\n-/* Media Queries\n-\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n-/*\n-Note: The best way to structure the use of media queries is to create the queries\n-near the relevant code. For example, if you wanted to change the styles for buttons\n-on small devices, paste the mobile query code up in the buttons section and style it\n-there.\n-*/\n-\n-\n-/* Larger than mobile */\n-@media (min-width: 400px) {}\n-\n-/* Larger than phablet (also point when grid becomes active) */\n-@media (min-width: 550px) {}\n-\n-/* Larger than tablet */\n-@media (min-width: 750px) {}\n-\n-/* Larger than desktop */\n-@media (min-width: 1000px) {}\n-\n-/* Larger than Desktop HD */\n-@media (min-width: 1200px) {}\n' |
| b |
| diff -r 8a87a2c44d09 -r 628f82e72d72 data/js/custom.js --- a/data/js/custom.js Fri Aug 21 12:37:54 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() { - $("#overlay").hide(); - }); -} -); |
| b |
| diff -r 8a87a2c44d09 -r 628f82e72d72 data/js/jquery-1.11.3.min.js --- a/data/js/jquery-1.11.3.min.js Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,5 +0,0 @@\n-/*! jQuery v1.11.3 | (c) 2005, 2015 jQuery Foundation, Inc. | jquery.org/license */\n-!function(a,b){"object"==typeof module&&"object"==typeof module.exports?module.exports=a.document?b(a,!0):function(a){if(!a.document)throw new Error("jQuery requires a window with a document");return b(a)}:b(a)}("undefined"!=typeof window?window:this,function(a,b){var c=[],d=c.slice,e=c.concat,f=c.push,g=c.indexOf,h={},i=h.toString,j=h.hasOwnProperty,k={},l="1.11.3",m=function(a,b){return new m.fn.init(a,b)},n=/^[\\s\\uFEFF\\xA0]+|[\\s\\uFEFF\\xA0]+$/g,o=/^-ms-/,p=/-([\\da-z])/gi,q=function(a,b){return b.toUpperCase()};m.fn=m.prototype={jquery:l,constructor:m,selector:"",length:0,toArray:function(){return d.call(this)},get:function(a){return null!=a?0>a?this[a+this.length]:this[a]:d.call(this)},pushStack:function(a){var b=m.merge(this.constructor(),a);return b.prevObject=this,b.context=this.context,b},each:function(a,b){return m.each(this,a,b)},map:function(a){return 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| diff -r 8a87a2c44d09 -r 628f82e72d72 data/js/jquery.tablesorter.min.js --- a/data/js/jquery.tablesorter.min.js Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,4 +0,0 @@\n-\n-(function($){$.extend({tablesorter:new\n-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 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| diff -r 8a87a2c44d09 -r 628f82e72d72 data/ribocount.html --- a/data/ribocount.html Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 data/ribocount_index.html --- a/data/ribocount_index.html Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 data/riboplot.html --- a/data/riboplot.html Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 docs/_static/alabaster.css_t --- a/docs/_static/alabaster.css_t Fri Aug 21 12:37:54 2015 +0100 +++ b/docs/_static/alabaster.css_t Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -105,8 +105,8 @@ div.sphinxsidebarwrapper p.logo { padding: 0; - margin: -10px 0 0 0px; - text-align: center; + margin: -10px 0 10px 0px; + text-align: left; } div.sphinxsidebarwrapper h1.logo { @@ -609,4 +609,4 @@ div.sphinxsidebar #searchbox input[type="submit"] { width: 40px; -} \ No newline at end of file +} |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 docs/_static/riboplot-logo.png |
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| Binary file docs/_static/riboplot-logo.png has changed |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 docs/authors.rst --- a/docs/authors.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/docs/authors.rst Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -1,13 +1,1 @@ -======= -Credits -======= - -Development Lead ----------------- - -* Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> - -Contributors ------------- - -None yet. Why not be the first? \ No newline at end of file +.. include:: ../AUTHORS.rst |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 docs/conf.py --- a/docs/conf.py Fri Aug 21 12:37:54 2015 +0100 +++ b/docs/conf.py Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -135,11 +135,11 @@ # A shorter title for the navigation bar. Default is the same as # html_title. -#html_short_title = None +html_short_title = 'RiboPlot' # The name of an image file (relative to this directory) to place at the # top of the sidebar. -#html_logo = None +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 @@ -154,7 +154,7 @@ # 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' +html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 docs/contributing.rst --- a/docs/contributing.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/docs/contributing.rst Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -1,111 +1,1 @@ -============ -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 +.. include:: ../CONTRIBUTING.rst |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 docs/history.rst --- a/docs/history.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/docs/history.rst Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -1,9 +1,1 @@ -.. :changelog: - -History -======= - -0.1.0 (2015-08-05) ---------------------- - -* First release on PyPI. +.. include:: ../HISTORY.rst |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 docs/index.rst --- a/docs/index.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/docs/index.rst Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -15,9 +15,16 @@ installation usage contributing + todo authors history +API: + +.. toctree:: + + modules + Indices and tables ================== |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 docs/installation.rst --- a/docs/installation.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/docs/installation.rst Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -1,7 +1,6 @@ ============ Installation ============ - At the command line:: $ easy_install riboplot @@ -9,4 +8,14 @@ Or, if you have virtualenvwrapper installed:: $ mkvirtualenv riboplot - $ pip install riboplot \ No newline at end of file + $ 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 |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 docs/readme.rst --- a/docs/readme.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/docs/readme.rst Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -1,28 +1,1 @@ -=============================== -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: BSD license. - -Documentation: https://riboplot.readthedocs.org. - +.. include:: ../README.rst |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 docs/riboplot.rst --- a/docs/riboplot.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/docs/riboplot.rst Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -36,15 +36,6 @@ :undoc-members: :show-inheritance: -riboplot.riboplot_multi module ------------------------------- - -.. automodule:: riboplot.riboplot_multi - :members: - :undoc-members: - :show-inheritance: - - Module contents --------------- |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 docs/todo.rst --- a/docs/todo.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/docs/todo.rst Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -1,38 +1,6 @@ -Outline -------- -Log information by default -Errors to stderr +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. -Arguments ---------- --b ribo_file --f transcriptome_fasta --t transcript_name --n rna_file --l read_length --s read_offset --m html_file --o output_path --d debug - -Tests ------ - -Check arguments -............... -* BAM file valid (should be indexed for fetch to work) -* FASTA file should be valid -* Transcript name should exist in both BAM and FASTA (riboplot: yes, ribocount: no). -* If RNA file is provided, bedtools should exist in PATH -* Read length should be a valid integer (must exist in BAM) -* Read offset - positive integer (can't exceed ?) -* Should be possible to get codon positions. - - -Notes ------ -* No way to check if input BAM is RNA-Seq/Ribo-Seq (plot will still be generated in either case) -* No way to check if BAM is sorted - - |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 docs/usage.rst --- a/docs/usage.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/docs/usage.rst Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -10,57 +10,60 @@ 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. 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`` +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. +++++++++++++++++++++++++ +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). +++++++++++++++++++++++++++++++++++++++++ +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. +++++++++++++++++++++++++++++++++++++++++++++ +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. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +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. ++++++++++++++++++++++++++++++++++++++++++++++ +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) - 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). - 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 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). - The color codes are start (white) and stop (dark gray). +.. image:: ../images/riboplot.png - .. image:: ../images/riboplot.png - -2. RiboSeq read counts in 3 frames for each position in the transcript (CSV) +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: python riboplot.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA -t TEXT + 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] @@ -105,29 +108,29 @@ 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. - 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`` +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. +++++++++++++++++++++++++ +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. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +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. ++++++++++++++++++++++++++++++++++++++++++++++ +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. @@ -140,7 +143,7 @@ ............ ``ribocount`` can also be run on the command line. The usage is :: - usage: python ribocount.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l INTEGER] + 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 @@ -172,3 +175,6 @@ -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA FASTA format file of the transcriptome +.. links +.. _RiboGalaxy: http://ribogalaxy.ucc.ie + |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 requirements.txt --- a/requirements.txt Fri Aug 21 12:37:54 2015 +0100 +++ b/requirements.txt Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -1,1 +1,12 @@ -wheel==0.23.0 \ No newline at end of file +argparse==1.2.1 +backports.ssl-match-hostname==3.4.0.2 +certifi==2015.04.28 +matplotlib==1.3.1 +nose==1.3.7 +numpy==1.9.2 +pyparsing==2.0.3 +pysam==0.8.3 +python-dateutil==2.4.2 +six==1.9.0 +tornado==4.2.1 +wsgiref==0.1.2 |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot.egg-info/PKG-INFO --- a/riboplot.egg-info/PKG-INFO Fri Aug 21 12:37:54 2015 +0100 +++ b/riboplot.egg-info/PKG-INFO Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -5,7 +5,7 @@ Home-page: https://github.com/vimalkumarvelayudhan/riboplot Author: Vimalkumar Velayudhan Author-email: vimalkumarvelayudhan@gmail.com -License: BSD +License: GPL Description: =============================== RiboPlot =============================== @@ -30,7 +30,7 @@ For help on using these programs, please refer to :ref:`usage`. - Free software: BSD license. + Free software: GPL license. Documentation: https://riboplot.readthedocs.org. @@ -41,7 +41,7 @@ History ======= - 0.1.0 (2015-08-05) + 0.1.0 (2015-08-24) --------------------- * First release on PyPI. @@ -55,6 +55,3 @@ Classifier: Programming Language :: Python :: 2 Classifier: Programming Language :: Python :: 2.6 Classifier: Programming Language :: Python :: 2.7 -Classifier: Programming Language :: Python :: 3 -Classifier: Programming Language :: Python :: 3.3 -Classifier: Programming Language :: Python :: 3.4 |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot.egg-info/SOURCES.txt --- a/riboplot.egg-info/SOURCES.txt Fri Aug 21 12:37:54 2015 +0100 +++ b/riboplot.egg-info/SOURCES.txt Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -24,30 +24,37 @@ riboplot/ribocore.py riboplot/ribocount.py riboplot/riboplot.py -riboplot/riboplot_multi.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 -tests/.test_ribocount.py.swp +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 -tests/data/5hRPF.bam -tests/data/5hRPF.bam.bai -tests/data/5hRPFsorted.bam -tests/data/5hRPFsorted.bam.bai -tests/data/5hmRNA.bam -tests/data/5hmRNAsorted.bam -tests/data/ribocount.html -tests/data/ribocount_index.html -tests/data/riboplot.html -tests/data/unrelated.fna -tests/data/unrelated.fna.fai -tests/data/zebrafish.fna -tests/data/zebrafish.fna.fai \ No newline at end of file +tests/.ropeproject/objectdb \ No newline at end of file |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot.egg-info/entry_points.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot.egg-info/entry_points.txt Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -0,0 +1,4 @@ +[console_scripts] +riboplot = riboplot.riboplot:run +ribocount = riboplot.ribocount:run + |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot.egg-info/requires.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot.egg-info/requires.txt Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -0,0 +1,2 @@ +matplotlib==1.3.1 +pysam==0.8.3 \ No newline at end of file |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/config.py --- a/riboplot/config.py Fri Aug 21 12:37:54 2015 +0100 +++ b/riboplot/config.py Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -6,14 +6,15 @@ # 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""" - DATA_DIR = os.path.join(Config.APP_DIR, 'tests/data') + TEST_DATA_DIR = os.path.join(Config.APP_DIR, 'tests/data') class ProductionConfig(Config): """Production configuration""" - # not used now - DATA_DIR = os.path.join(Config.APP_DIR, 'data') + # Additional variables can be listed here + pass |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/data/css/asc.gif |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/data/css/bg.gif |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/data/css/custom.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/data/css/custom.css Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -0,0 +1,61 @@ +.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 |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/data/css/desc.gif |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/data/css/normalize.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/data/css/normalize.css Wed Aug 26 16:37:10 2015 +0100 |
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| b'@@ -0,0 +1,427 @@\n+/*! normalize.css v3.0.2 | MIT License | git.io/normalize */\n+\n+/**\n+ * 1. Set default font family to sans-serif.\n+ * 2. Prevent iOS text size adjust after orientation change, without disabling\n+ * user zoom.\n+ */\n+\n+html {\n+ font-family: sans-serif; /* 1 */\n+ -ms-text-size-adjust: 100%; /* 2 */\n+ -webkit-text-size-adjust: 100%; /* 2 */\n+}\n+\n+/**\n+ * Remove default margin.\n+ */\n+\n+body {\n+ margin: 0;\n+}\n+\n+/* HTML5 display definitions\n+ ========================================================================== */\n+\n+/**\n+ * Correct `block` display not defined for any HTML5 element in IE 8/9.\n+ * Correct `block` display not defined for `details` or `summary` in IE 10/11\n+ * and Firefox.\n+ * Correct `block` display not defined for `main` in IE 11.\n+ */\n+\n+article,\n+aside,\n+details,\n+figcaption,\n+figure,\n+footer,\n+header,\n+hgroup,\n+main,\n+menu,\n+nav,\n+section,\n+summary {\n+ display: block;\n+}\n+\n+/**\n+ * 1. Correct `inline-block` display not defined in IE 8/9.\n+ * 2. Normalize vertical alignment of `progress` in Chrome, Firefox, and Opera.\n+ */\n+\n+audio,\n+canvas,\n+progress,\n+video {\n+ display: inline-block; /* 1 */\n+ vertical-align: baseline; /* 2 */\n+}\n+\n+/**\n+ * Prevent modern browsers from displaying `audio` without controls.\n+ * Remove excess height in iOS 5 devices.\n+ */\n+\n+audio:not([controls]) {\n+ display: none;\n+ height: 0;\n+}\n+\n+/**\n+ * Address `[hidden]` styling not present in IE 8/9/10.\n+ * Hide the `template` element in IE 8/9/11, Safari, and Firefox < 22.\n+ */\n+\n+[hidden],\n+template {\n+ display: none;\n+}\n+\n+/* Links\n+ ========================================================================== */\n+\n+/**\n+ * Remove the gray background color from active links in IE 10.\n+ */\n+\n+a {\n+ background-color: transparent;\n+}\n+\n+/**\n+ * Improve readability when focused and also mouse hovered in all browsers.\n+ */\n+\n+a:active,\n+a:hover {\n+ outline: 0;\n+}\n+\n+/* Text-level semantics\n+ ========================================================================== */\n+\n+/**\n+ * Address styling not present in IE 8/9/10/11, Safari, and Chrome.\n+ */\n+\n+abbr[title] {\n+ border-bottom: 1px dotted;\n+}\n+\n+/**\n+ * Address style set to `bolder` in Firefox 4+, Safari, and Chrome.\n+ */\n+\n+b,\n+strong {\n+ font-weight: bold;\n+}\n+\n+/**\n+ * Address styling not present in Safari and Chrome.\n+ */\n+\n+dfn {\n+ font-style: italic;\n+}\n+\n+/**\n+ * Address variable `h1` font-size and margin within `section` and `article`\n+ * contexts in Firefox 4+, Safari, and Chrome.\n+ */\n+\n+h1 {\n+ font-size: 2em;\n+ margin: 0.67em 0;\n+}\n+\n+/**\n+ * Address styling not present in IE 8/9.\n+ */\n+\n+mark {\n+ background: #ff0;\n+ color: #000;\n+}\n+\n+/**\n+ * Address inconsistent and variable font size in all browsers.\n+ */\n+\n+small {\n+ font-size: 80%;\n+}\n+\n+/**\n+ * Prevent `sub` and `sup` affecting `line-height` in all browsers.\n+ */\n+\n+sub,\n+sup {\n+ font-size: 75%;\n+ line-height: 0;\n+ position: relative;\n+ vertical-align: baseline;\n+}\n+\n+sup {\n+ top: -0.5em;\n+}\n+\n+sub {\n+ bottom: -0.25em;\n+}\n+\n+/* Embedded content\n+ ========================================================================== */\n+\n+/**\n+ * Remove border when inside `a` element in IE 8/9/10.\n+ */\n+\n+img {\n+ border: 0;\n+}\n+\n+/**\n+ * Correct overflow not hidden in IE 9/10/11.\n+ */\n+\n+svg:not(:root) {\n+ overflow: hidden;\n+}\n+\n+/* Grouping content\n+ ========================================================================== */\n+\n+/**\n+ * Address margin not present in IE 8/9 and Safari.\n+ */\n+\n+figure {\n+ margin: 1em 40px;\n+}\n+\n+/**\n+ * Address differences between Firefox and other browsers.\n+ */\n+\n+hr {\n+ -moz-box-sizing: content-box;\n+ box-sizing: content-box;\n+ height: 0;\n+}\n+\n+/**\n+ * Contain overflow in all browsers.\n+ */\n+\n+pre {\n+ overflow: auto;\n+}\n+\n+/**\n+ * Address odd `em`-unit font size rendering in all browsers.\n+ */\n+\n+code,\n+kbd,\n+pre,\n+samp {\n+ font-family: monospace, monospace;\n+ font-size: 1em;\n+}\n+\n+/* Forms\n+ ======================================'..b' of disabled elements.\n+ * 2. Correct font properties not being inherited.\n+ * 3. Address margins set differently in Firefox 4+, Safari, and Chrome.\n+ */\n+\n+button,\n+input,\n+optgroup,\n+select,\n+textarea {\n+ color: inherit; /* 1 */\n+ font: inherit; /* 2 */\n+ margin: 0; /* 3 */\n+}\n+\n+/**\n+ * Address `overflow` set to `hidden` in IE 8/9/10/11.\n+ */\n+\n+button {\n+ overflow: visible;\n+}\n+\n+/**\n+ * Address inconsistent `text-transform` inheritance for `button` and `select`.\n+ * All other form control elements do not inherit `text-transform` values.\n+ * Correct `button` style inheritance in Firefox, IE 8/9/10/11, and Opera.\n+ * Correct `select` style inheritance in Firefox.\n+ */\n+\n+button,\n+select {\n+ text-transform: none;\n+}\n+\n+/**\n+ * 1. Avoid the WebKit bug in Android 4.0.* where (2) destroys native `audio`\n+ * and `video` controls.\n+ * 2. Correct inability to style clickable `input` types in iOS.\n+ * 3. Improve usability and consistency of cursor style between image-type\n+ * `input` and others.\n+ */\n+\n+button,\n+html input[type="button"], /* 1 */\n+input[type="reset"],\n+input[type="submit"] {\n+ -webkit-appearance: button; /* 2 */\n+ cursor: pointer; /* 3 */\n+}\n+\n+/**\n+ * Re-set default cursor for disabled elements.\n+ */\n+\n+button[disabled],\n+html input[disabled] {\n+ cursor: default;\n+}\n+\n+/**\n+ * Remove inner padding and border in Firefox 4+.\n+ */\n+\n+button::-moz-focus-inner,\n+input::-moz-focus-inner {\n+ border: 0;\n+ padding: 0;\n+}\n+\n+/**\n+ * Address Firefox 4+ setting `line-height` on `input` using `!important` in\n+ * the UA stylesheet.\n+ */\n+\n+input {\n+ line-height: normal;\n+}\n+\n+/**\n+ * It\'s recommended that you don\'t attempt to style these elements.\n+ * Firefox\'s implementation doesn\'t respect box-sizing, padding, or width.\n+ *\n+ * 1. Address box sizing set to `content-box` in IE 8/9/10.\n+ * 2. Remove excess padding in IE 8/9/10.\n+ */\n+\n+input[type="checkbox"],\n+input[type="radio"] {\n+ box-sizing: border-box; /* 1 */\n+ padding: 0; /* 2 */\n+}\n+\n+/**\n+ * Fix the cursor style for Chrome\'s increment/decrement buttons. For certain\n+ * `font-size` values of the `input`, it causes the cursor style of the\n+ * decrement button to change from `default` to `text`.\n+ */\n+\n+input[type="number"]::-webkit-inner-spin-button,\n+input[type="number"]::-webkit-outer-spin-button {\n+ height: auto;\n+}\n+\n+/**\n+ * 1. Address `appearance` set to `searchfield` in Safari and Chrome.\n+ * 2. Address `box-sizing` set to `border-box` in Safari and Chrome\n+ * (include `-moz` to future-proof).\n+ */\n+\n+input[type="search"] {\n+ -webkit-appearance: textfield; /* 1 */\n+ -moz-box-sizing: content-box;\n+ -webkit-box-sizing: content-box; /* 2 */\n+ box-sizing: content-box;\n+}\n+\n+/**\n+ * Remove inner padding and search cancel button in Safari and Chrome on OS X.\n+ * Safari (but not Chrome) clips the cancel button when the search input has\n+ * padding (and `textfield` appearance).\n+ */\n+\n+input[type="search"]::-webkit-search-cancel-button,\n+input[type="search"]::-webkit-search-decoration {\n+ -webkit-appearance: none;\n+}\n+\n+/**\n+ * Define consistent border, margin, and padding.\n+ */\n+\n+fieldset {\n+ border: 1px solid #c0c0c0;\n+ margin: 0 2px;\n+ padding: 0.35em 0.625em 0.75em;\n+}\n+\n+/**\n+ * 1. Correct `color` not being inherited in IE 8/9/10/11.\n+ * 2. Remove padding so people aren\'t caught out if they zero out fieldsets.\n+ */\n+\n+legend {\n+ border: 0; /* 1 */\n+ padding: 0; /* 2 */\n+}\n+\n+/**\n+ * Remove default vertical scrollbar in IE 8/9/10/11.\n+ */\n+\n+textarea {\n+ overflow: auto;\n+}\n+\n+/**\n+ * Don\'t inherit the `font-weight` (applied by a rule above).\n+ * NOTE: the default cannot safely be changed in Chrome and Safari on OS X.\n+ */\n+\n+optgroup {\n+ font-weight: bold;\n+}\n+\n+/* Tables\n+ ========================================================================== */\n+\n+/**\n+ * Remove most spacing between table cells.\n+ */\n+\n+table {\n+ border-collapse: collapse;\n+ border-spacing: 0;\n+}\n+\n+td,\n+th {\n+ padding: 0;\n+}\n\\ No newline at end of file\n' |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/data/css/skeleton.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/data/css/skeleton.css Wed Aug 26 16:37:10 2015 +0100 |
| [ |
| b'@@ -0,0 +1,419 @@\n+/*\n+* Skeleton V2.0.4\n+* Copyright 2014, Dave Gamache\n+* www.getskeleton.com\n+* Free to use under the MIT license.\n+* http://www.opensource.org/licenses/mit-license.php\n+* 12/29/2014\n+*/\n+\n+\n+/* Table of contents\n+\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\n+- Grid\n+- Base Styles\n+- Typography\n+- Links\n+- Buttons\n+- Forms\n+- Lists\n+- Code\n+- Tables\n+- Spacing\n+- Utilities\n+- Clearing\n+- Media Queries\n+*/\n+\n+\n+/* Grid\n+\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n+.container {\n+ position: relative;\n+ width: 100%;\n+ max-width: 960px;\n+ margin: 0 auto;\n+ padding: 0 20px;\n+ box-sizing: border-box; }\n+.column,\n+.columns {\n+ width: 100%;\n+ float: left;\n+ box-sizing: border-box; }\n+\n+/* For devices larger than 400px */\n+@media (min-width: 400px) {\n+ .container {\n+ width: 85%;\n+ padding: 0; }\n+}\n+\n+/* For devices larger than 550px */\n+@media (min-width: 550px) {\n+ .container {\n+ width: 80%; }\n+ .column,\n+ .columns {\n+ margin-left: 4%; }\n+ .column:first-child,\n+ .columns:first-child {\n+ margin-left: 0; }\n+\n+ .one.column,\n+ .one.columns { width: 4.66666666667%; }\n+ .two.columns { width: 13.3333333333%; }\n+ .three.columns { width: 22%; }\n+ .four.columns { width: 30.6666666667%; }\n+ .five.columns { width: 39.3333333333%; }\n+ .six.columns { width: 48%; }\n+ .seven.columns { width: 56.6666666667%; }\n+ .eight.columns { width: 65.3333333333%; }\n+ .nine.columns { width: 74.0%; }\n+ .ten.columns { width: 82.6666666667%; }\n+ .eleven.columns { width: 91.3333333333%; }\n+ .twelve.columns { width: 100%; margin-left: 0; }\n+\n+ .one-third.column { width: 30.6666666667%; }\n+ .two-thirds.column { width: 65.3333333333%; }\n+\n+ .one-half.column { width: 48%; }\n+\n+ /* Offsets */\n+ .offset-by-one.column,\n+ .offset-by-one.columns { margin-left: 8.66666666667%; }\n+ .offset-by-two.column,\n+ .offset-by-two.columns { margin-left: 17.3333333333%; }\n+ .offset-by-three.column,\n+ .offset-by-three.columns { margin-left: 26%; }\n+ .offset-by-four.column,\n+ .offset-by-four.columns { margin-left: 34.6666666667%; }\n+ .offset-by-five.column,\n+ .offset-by-five.columns { margin-left: 43.3333333333%; }\n+ .offset-by-six.column,\n+ .offset-by-six.columns { margin-left: 52%; }\n+ .offset-by-seven.column,\n+ .offset-by-seven.columns { margin-left: 60.6666666667%; }\n+ .offset-by-eight.column,\n+ .offset-by-eight.columns { margin-left: 69.3333333333%; }\n+ .offset-by-nine.column,\n+ .offset-by-nine.columns { margin-left: 78.0%; }\n+ .offset-by-ten.column,\n+ .offset-by-ten.columns { margin-left: 86.6666666667%; }\n+ .offset-by-eleven.column,\n+ .offset-by-eleven.columns { margin-left: 95.3333333333%; }\n+\n+ .offset-by-one-third.column,\n+ .offset-by-one-third.columns { margin-left: 34.6666666667%; }\n+ .offset-by-two-thirds.column,\n+ .offset-by-two-thirds.columns { margin-left: 69.3333333333%; }\n+\n+ .offset-by-one-half.column,\n+ .offset-by-one-half.columns { margin-left: 52%; }\n+\n+}\n+\n+\n+/* Base Styles\n+\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n+/* NOTE\n+html is set to 62.5% so that all the REM measurements throughout Skeleton\n+are based on 10px sizing. So basically 1.5rem = 15px :) */\n+html {\n+ font-size: 62.5%; }\n+body {\n+ font-size: 1.5em; /* currently ems cause chrome bug '..b'none; }\n+textarea {\n+ min-height: 65px;\n+ padding-top: 6px;\n+ padding-bottom: 6px; }\n+input[type="email"]:focus,\n+input[type="number"]:focus,\n+input[type="search"]:focus,\n+input[type="text"]:focus,\n+input[type="tel"]:focus,\n+input[type="url"]:focus,\n+input[type="password"]:focus,\n+textarea:focus,\n+select:focus {\n+ border: 1px solid #33C3F0;\n+ outline: 0; }\n+label,\n+legend {\n+ display: block;\n+ margin-bottom: .5rem;\n+ font-weight: 600; }\n+fieldset {\n+ padding: 0;\n+ border-width: 0; }\n+input[type="checkbox"],\n+input[type="radio"] {\n+ display: inline; }\n+label > .label-body {\n+ display: inline-block;\n+ margin-left: .5rem;\n+ font-weight: normal; }\n+\n+\n+/* Lists\n+\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n+ul {\n+ list-style: circle inside; }\n+ol {\n+ list-style: decimal inside; }\n+ol, ul {\n+ padding-left: 0;\n+ margin-top: 0; }\n+ul ul,\n+ul ol,\n+ol ol,\n+ol ul {\n+ margin: 1.5rem 0 1.5rem 3rem;\n+ font-size: 90%; }\n+li {\n+ margin-bottom: 1rem; }\n+\n+\n+/* Code\n+\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n+code {\n+ padding: .2rem .5rem;\n+ margin: 0 .2rem;\n+ font-size: 90%;\n+ white-space: nowrap;\n+ background: #F1F1F1;\n+ border: 1px solid #E1E1E1;\n+ border-radius: 4px; }\n+pre > code {\n+ display: block;\n+ padding: 1rem 1.5rem;\n+ white-space: pre; }\n+\n+\n+/* Tables\n+\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n+th,\n+td {\n+ padding: 12px 15px;\n+ text-align: left;\n+ border-bottom: 1px solid #E1E1E1; }\n+\n+/*th:first-child,\n+td:first-child {\n+ padding-left: 0; }\n+th:last-child,\n+td:last-child {\n+ padding-right: 0; }\n+*/\n+\n+/* Spacing\n+\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n+button,\n+.button {\n+ margin-bottom: 1rem; }\n+input,\n+textarea,\n+select,\n+fieldset {\n+ margin-bottom: 1.5rem; }\n+pre,\n+blockquote,\n+dl,\n+figure,\n+table,\n+p,\n+ul,\n+ol,\n+form {\n+ margin-bottom: 2.5rem; }\n+\n+\n+/* Utilities\n+\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n+.u-full-width {\n+ width: 100%;\n+ box-sizing: border-box; }\n+.u-max-full-width {\n+ max-width: 100%;\n+ box-sizing: border-box; }\n+.u-pull-right {\n+ float: right; }\n+.u-pull-left {\n+ float: left; }\n+\n+\n+/* Misc\n+\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n+hr {\n+ margin-top: 3rem;\n+ margin-bottom: 3.5rem;\n+ border-width: 0;\n+ border-top: 1px solid #E1E1E1; }\n+\n+\n+/* Clearing\n+\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n+\n+/* Self Clearing Goodness */\n+.container:after,\n+.row:after,\n+.u-cf {\n+ content: "";\n+ display: table;\n+ clear: both; }\n+\n+\n+/* Media Queries\n+\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93\xe2\x80\x93 */\n+/*\n+Note: The best way to structure the use of media queries is to create the queries\n+near the relevant code. For example, if you wanted to change the styles for buttons\n+on small devices, paste the mobile query code up in the buttons section and style it\n+there.\n+*/\n+\n+\n+/* Larger than mobile */\n+@media (min-width: 400px) {}\n+\n+/* Larger than phablet (also point when grid becomes active) */\n+@media (min-width: 550px) {}\n+\n+/* Larger than tablet */\n+@media (min-width: 750px) {}\n+\n+/* Larger than desktop */\n+@media (min-width: 1000px) {}\n+\n+/* Larger than Desktop HD */\n+@media (min-width: 1200px) {}\n' |
| b |
| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/data/js/custom.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/data/js/custom.js Wed Aug 26 16:37:10 2015 +0100 |
| [ |
| @@ -0,0 +1,11 @@ +$(document).ready(function() +{ + $("#counts-table").tablesorter({sortList: [[2,1]]}); + //assign the sortStart event + $("#counts-table").bind("sortStart", function() { + $("#overlay").show(); + }).bind("sortEnd",function() { + $("#overlay").hide(); + }); +} +); |
| b |
| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/data/js/jquery-1.11.3.min.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/data/js/jquery-1.11.3.min.js Wed Aug 26 16:37:10 2015 +0100 |
| [ |
| b'@@ -0,0 +1,5 @@\n+/*! jQuery v1.11.3 | (c) 2005, 2015 jQuery Foundation, Inc. | jquery.org/license */\n+!function(a,b){"object"==typeof module&&"object"==typeof module.exports?module.exports=a.document?b(a,!0):function(a){if(!a.document)throw new Error("jQuery requires a window with a document");return b(a)}:b(a)}("undefined"!=typeof window?window:this,function(a,b){var c=[],d=c.slice,e=c.concat,f=c.push,g=c.indexOf,h={},i=h.toString,j=h.hasOwnProperty,k={},l="1.11.3",m=function(a,b){return new m.fn.init(a,b)},n=/^[\\s\\uFEFF\\xA0]+|[\\s\\uFEFF\\xA0]+$/g,o=/^-ms-/,p=/-([\\da-z])/gi,q=function(a,b){return b.toUpperCase()};m.fn=m.prototype={jquery:l,constructor:m,selector:"",length:0,toArray:function(){return d.call(this)},get:function(a){return null!=a?0>a?this[a+this.length]:this[a]:d.call(this)},pushStack:function(a){var b=m.merge(this.constructor(),a);return b.prevObject=this,b.context=this.context,b},each:function(a,b){return m.each(this,a,b)},map:function(a){return 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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/data/js/jquery.tablesorter.min.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/data/js/jquery.tablesorter.min.js Wed Aug 26 16:37:10 2015 +0100 |
| [ |
| b'@@ -0,0 +1,4 @@\n+\n+(function($){$.extend({tablesorter:new\n+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 row:\'+rowIndex);}}else{keepLooking=false;}}for(var i=1;i<l;i++){if(parsers[i].is(nodeValue,table,node)){return parsers[i];}}return parsers[0];}function getNodeFromRowAndCellIndex(rows,rowIndex,cellIndex){return rows[rowIndex].cells[cellIndex];}function trimAndGetNodeText(config,node){return $.trim(getElementText(config,node));}function getParserById(name){var l=parsers.length;for(var i=0;i<l;i++){if(parsers[i].id.toLowerCase()==name.toLowerCase()){return parsers[i];}}return false;}function buildCache(table){if(table.config.debug){var cacheTime=new Date();}var totalRows=(table.tBodies[0]&&table.tBodies[0].rows.length)||0,totalCells=(table.tBodies[0].rows[0]&&table.tBodies[0].rows[0].cells.length)||0,parsers=table.config.parsers,cache={row:[],normalized:[]};for(var i=0;i<totalRows;++i){var c=$(table.tBodies[0].rows[i]),cols=[];if(c.hasClass(table.config.cssChildRow)){cache.row[cache.row.length-1]=cache.row[cache.row.length-1].add(c);continue;}cache.row.push(c);for(var j=0;j<totalCells;++j){cols.push(parsers[j].format(getElementText(table.config,c[0].cells[j]),table,c[0].cells[j]));}cols.push(cache.normalized.length);cache.normalized.push(cols);cols=null;};if(table.config.debug){benchmark("Building cache for "+totalRows+" rows:",cacheTime);}return cache;};function getElementText(config,node){var text="";if(!node)return"";if(!config.supportsTextContent)config.supportsTextContent=node.textContent||false;if(config.textExtraction=="simple"){if(config.supportsTextContent){text=node.textContent;}else{if(node.childNodes[0]&&node.childNodes[0].hasChildNodes()){text=node.childNodes[0].innerHTML;}else{text=node.innerHTML;}}}else{if(typeof(config.textExtraction)=="function"){text=config.textExtraction(node);}else{text=$(node).text();}}return text;}function appendToTable(table,cache){if(table.config.debug){var appendTime=new Date()}var c=cache,r=c.row,n=c.normalized,totalRows=n.length,checkCell=(n[0].length-1),tableBody=$(table.tBodies[0]),rows=[];for(var i=0;i<totalRows;i++){var pos=n[i][checkCell];rows.push(r[pos]);if(!table.config.appender){var l=r[pos].length;for(var j=0;j<l;j++){tableBody[0].appendChild(r[pos][j]);}}}if(table.config.appender){table.config.appende'..b'rtList.length>0){$this.trigger("sorton",[config.sortList]);}applyWidget(this);});};this.addParser=function(parser){var l=parsers.length,a=true;for(var i=0;i<l;i++){if(parsers[i].id.toLowerCase()==parser.id.toLowerCase()){a=false;}}if(a){parsers.push(parser);};};this.addWidget=function(widget){widgets.push(widget);};this.formatFloat=function(s){var i=parseFloat(s);return(isNaN(i))?0:i;};this.formatInt=function(s){var i=parseInt(s);return(isNaN(i))?0:i;};this.isDigit=function(s,config){return/^[-+]?\\d*$/.test($.trim(s.replace(/[,.\']/g,\'\')));};this.clearTableBody=function(table){if($.browser.msie){function empty(){while(this.firstChild)this.removeChild(this.firstChild);}empty.apply(table.tBodies[0]);}else{table.tBodies[0].innerHTML="";}};}});$.fn.extend({tablesorter:$.tablesorter.construct});var ts=$.tablesorter;ts.addParser({id:"text",is:function(s){return true;},format:function(s){return $.trim(s.toLocaleLowerCase());},type:"text"});ts.addParser({id:"digit",is:function(s,table){var c=table.config;return $.tablesorter.isDigit(s,c);},format:function(s){return $.tablesorter.formatFloat(s);},type:"numeric"});ts.addParser({id:"currency",is:function(s){return/^[\xc2\xa3$\xe2\x82\xac?.]/.test(s);},format:function(s){return $.tablesorter.formatFloat(s.replace(new RegExp(/[\xc2\xa3$\xe2\x82\xac]/g),""));},type:"numeric"});ts.addParser({id:"ipAddress",is:function(s){return/^\\d{2,3}[\\.]\\d{2,3}[\\.]\\d{2,3}[\\.]\\d{2,3}$/.test(s);},format:function(s){var a=s.split("."),r="",l=a.length;for(var i=0;i<l;i++){var item=a[i];if(item.length==2){r+="0"+item;}else{r+=item;}}return $.tablesorter.formatFloat(r);},type:"numeric"});ts.addParser({id:"url",is:function(s){return/^(https?|ftp|file):\\/\\/$/.test(s);},format:function(s){return jQuery.trim(s.replace(new RegExp(/(https?|ftp|file):\\/\\//),\'\'));},type:"text"});ts.addParser({id:"isoDate",is:function(s){return/^\\d{4}[\\/-]\\d{1,2}[\\/-]\\d{1,2}$/.test(s);},format:function(s){return $.tablesorter.formatFloat((s!="")?new Date(s.replace(new RegExp(/-/g),"/")).getTime():"0");},type:"numeric"});ts.addParser({id:"percent",is:function(s){return/\\%$/.test($.trim(s));},format:function(s){return $.tablesorter.formatFloat(s.replace(new RegExp(/%/g),""));},type:"numeric"});ts.addParser({id:"usLongDate",is:function(s){return s.match(new RegExp(/^[A-Za-z]{3,10}\\.? [0-9]{1,2}, ([0-9]{4}|\'?[0-9]{2}) (([0-2]?[0-9]:[0-5][0-9])|([0-1]?[0-9]:[0-5][0-9]\\s(AM|PM)))$/));},format:function(s){return $.tablesorter.formatFloat(new Date(s).getTime());},type:"numeric"});ts.addParser({id:"shortDate",is:function(s){return/\\d{1,2}[\\/\\-]\\d{1,2}[\\/\\-]\\d{2,4}/.test(s);},format:function(s,table){var c=table.config;s=s.replace(/\\-/g,"/");if(c.dateFormat=="us"){s=s.replace(/(\\d{1,2})[\\/\\-](\\d{1,2})[\\/\\-](\\d{4})/,"$3/$1/$2");}else if (c.dateFormat == "pt") {s = s.replace(/(\\d{1,2})[\\/\\-](\\d{1,2})[\\/\\-](\\d{4})/, "$3/$2/$1");} else if(c.dateFormat=="uk"){s=s.replace(/(\\d{1,2})[\\/\\-](\\d{1,2})[\\/\\-](\\d{4})/,"$3/$2/$1");}else if(c.dateFormat=="dd/mm/yy"||c.dateFormat=="dd-mm-yy"){s=s.replace(/(\\d{1,2})[\\/\\-](\\d{1,2})[\\/\\-](\\d{2})/,"$1/$2/$3");}return $.tablesorter.formatFloat(new Date(s).getTime());},type:"numeric"});ts.addParser({id:"time",is:function(s){return/^(([0-2]?[0-9]:[0-5][0-9])|([0-1]?[0-9]:[0-5][0-9]\\s(am|pm)))$/.test(s);},format:function(s){return $.tablesorter.formatFloat(new Date("2000/01/01 "+s).getTime());},type:"numeric"});ts.addParser({id:"metadata",is:function(s){return false;},format:function(s,table,cell){var c=table.config,p=(!c.parserMetadataName)?\'sortValue\':c.parserMetadataName;return $(cell).metadata()[p];},type:"numeric"});ts.addWidget({id:"zebra",format:function(table){if(table.config.debug){var time=new Date();}var $tr,row=-1,odd;$("tr:visible",table.tBodies[0]).each(function(i){$tr=$(this);if(!$tr.hasClass(table.config.cssChildRow))row++;odd=(row%2==0);$tr.removeClass(table.config.widgetZebra.css[odd?0:1]).addClass(table.config.widgetZebra.css[odd?1:0])});if(table.config.debug){$.tablesorter.benchmark("Applying Zebra widget",time);}}});})(jQuery);\n' |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/data/ribocount.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/data/ribocount.html Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -0,0 +1,63 @@ +<!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> |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/data/ribocount_index.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/data/ribocount_index.html Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -0,0 +1,25 @@ +<!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 |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/data/riboplot.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/data/riboplot.html Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -0,0 +1,61 @@ +<!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 |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/ribocount.py --- a/riboplot/ribocount.py Fri Aug 21 12:37:54 2015 +0100 +++ b/riboplot/ribocount.py Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -129,7 +129,7 @@ else: log.info('No transcripts found') else: - with open(os.path.join(CONFIG.DATA_DIR, 'ribocount.html')) as g,\ + 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)) @@ -137,7 +137,7 @@ 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.DATA_DIR, asset) + 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)) @@ -152,11 +152,17 @@ os.chdir('../') log.debug('Writing HTML report') - with open(os.path.join(CONFIG.DATA_DIR, 'ribocount_index.html')) as j, open(args.html_file, 'w') as k: + 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') -if __name__ == '__main__': + +def run(): + """Run program""" parsed = create_parser() args = parsed.parse_args() main(args) + + +if __name__ == '__main__': + run() |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/riboplot.py --- a/riboplot/riboplot.py Fri Aug 21 12:37:54 2015 +0100 +++ b/riboplot/riboplot.py Wed Aug 26 16:37:10 2015 +0100 |
| [ |
| @@ -227,14 +227,14 @@ 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.DATA_DIR, 'riboplot.html')) as g, open(os.path.join(output_path, html_file), 'w') as h: + 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.DATA_DIR, 'css') + 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)) @@ -273,7 +273,7 @@ '\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(args.html_file) + fh = logging.FileHandler(html_file) fh.setLevel(logging.ERROR) fh.setFormatter(ErrorLogFormatter('%(message)s')) log.addHandler(fh) @@ -342,7 +342,13 @@ html_file=args.html_file, output_path=args.output_path) log.info('Finished!') -if __name__ == '__main__': + +def run(): + """Run program""" parsed = create_parser() args = parsed.parse_args() main(args) + + +if __name__ == '__main__': + run() |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/scripts/run_coverage.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/scripts/run_coverage.sh Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -0,0 +1,5 @@ +#!/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 |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/scripts/run_ribocount_sample.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/scripts/run_ribocount_sample.sh Wed Aug 26 16:37:10 2015 +0100 |
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| @@ -0,0 +1,6 @@ +#!/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 + |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/scripts/run_riboplot_sample.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/scripts/run_riboplot_sample.sh Wed Aug 26 16:37:10 2015 +0100 |
| b |
| @@ -0,0 +1,8 @@ +#!/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 + |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 riboplot/scripts/run_tests.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/scripts/run_tests.sh Wed Aug 26 16:37:10 2015 +0100 |
| b |
| @@ -0,0 +1,5 @@ +#!/bin/bash +# Run all tests + +echo "Please run this script from the main package directory else this would fail" +python setup.py test |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 run_coverage.sh --- a/run_coverage.sh Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -coverage run --source tests/test_riboplot.py --source riboplot setup.py test -coverage html |
| b |
| diff -r 8a87a2c44d09 -r 628f82e72d72 run_ribocount_sample.sh --- a/run_ribocount_sample.sh Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -#!/bin/bash -python riboplot/ribocount.py -b tests/data/5hRPFsorted.bam \ - -f tests/data/zebrafish.fna - |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 run_riboplot_sample.sh --- a/run_riboplot_sample.sh Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -#!/bin/bash -python riboplot/riboplot.py -b tests/data/5hRPFsorted.bam \ - -f tests/data/zebrafish.fna \ - -t 'gi|148357119|ref|NM_001098396.1|' \ -# -n tests/data/5hmRNAsorted.bam - |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 run_tests.sh --- a/run_tests.sh Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -#!/bin/bash -python setup.py test |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 setup.py --- a/setup.py Fri Aug 21 12:37:54 2015 +0100 +++ b/setup.py Wed Aug 26 16:37:10 2015 +0100 |
| [ |
| @@ -14,9 +14,7 @@ with open('HISTORY.rst') as history_file: history = history_file.read().replace('.. :changelog:', '') -requirements = [ - # TODO: put package requirements here -] +requirements = ['matplotlib==1.3.1', 'pysam==0.8.3'] test_requirements = [ # TODO: put package test requirements here @@ -35,23 +33,27 @@ ], package_dir={'riboplot': 'riboplot'}, - include_package_data=True, install_requires=requirements, - license="BSD", + license="GPL", zip_safe=False, keywords='riboplot', classifiers=[ 'Development Status :: 2 - Pre-Alpha', 'Intended Audience :: Developers', - 'License :: OSI Approved :: BSD License', + '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', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.3', - 'Programming Language :: Python :: 3.4', ], test_suite='tests', - tests_require=test_requirements -) \ No newline at end of file + 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']} +) |
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| diff -r 8a87a2c44d09 -r 628f82e72d72 tests/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/README.rst Wed Aug 26 16:37:10 2015 +0100 |
| b |
| @@ -0,0 +1,7 @@ +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 + |
| b |
| diff -r 8a87a2c44d09 -r 628f82e72d72 tests/test_ribocount.py --- a/tests/test_ribocount.py Fri Aug 21 12:37:54 2015 +0100 +++ b/tests/test_ribocount.py Wed Aug 26 16:37:10 2015 +0100 |
| b |
| @@ -8,12 +8,12 @@ CONFIG = ribocount.CONFIG = riboplot.config.TestingConfig() logging.disable(logging.CRITICAL) -RIBO_FILE = os.path.join(CONFIG.DATA_DIR, '5hRPFsorted.bam') -RNA_FILE = os.path.join(CONFIG.DATA_DIR, '5hmRNAsorted.bam') +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.DATA_DIR, 'zebrafish.fna') -TRANSCRIPTOME_FASTA_MINUS1 = os.path.join(CONFIG.DATA_DIR, 'zebrafish_minus1.fna') -UNRELATED_FASTA = os.path.join(CONFIG.DATA_DIR, 'unrelated.fna') +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): |
| b |
| diff -r 8a87a2c44d09 -r 628f82e72d72 tests/test_riboplot.py --- a/tests/test_riboplot.py Fri Aug 21 12:37:54 2015 +0100 +++ b/tests/test_riboplot.py Wed Aug 26 16:37:10 2015 +0100 |
| [ |
| @@ -10,11 +10,11 @@ CONFIG = riboplot.CONFIG = riboplot.config.TestingConfig() logging.disable(logging.CRITICAL) -RIBO_FILE = os.path.join(CONFIG.DATA_DIR, '5hRPFsorted.bam') -RNA_FILE = os.path.join(CONFIG.DATA_DIR, '5hmRNAsorted.bam') +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.DATA_DIR, 'zebrafish.fna') -TRANSCRIPTOME_FASTA_MINUS1 = os.path.join(CONFIG.DATA_DIR, 'zebrafish_minus1.fna') +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): @@ -97,7 +97,7 @@ 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', '/home/vimal/tmp/empty_tp/RiboSeq.bam', '-f', TRANSCRIPTOME_FASTA, + 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) |
