| Next changeset 1:1e9797878349 (2015-06-29) |
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Commit message:
First commit |
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added:
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 ribocount.xml riboplot.xml riboplot/__init__.py riboplot/config.py riboplot/core.py riboplot/ribocount.py riboplot/riboplot.py runtests.sh tests/__init__.py tests/test_plot.py tool_dependencies.xml |
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| diff -r 000000000000 -r ca58e9466cbf data/css/asc.gif |
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| diff -r 000000000000 -r ca58e9466cbf data/css/bg.gif |
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| Binary file data/css/bg.gif has changed |
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| diff -r 000000000000 -r ca58e9466cbf data/css/custom.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/css/custom.css Mon Jun 29 16:38:36 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 000000000000 -r ca58e9466cbf data/css/desc.gif |
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| diff -r 000000000000 -r ca58e9466cbf data/css/normalize.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/css/normalize.css Mon Jun 29 16:38:36 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 000000000000 -r ca58e9466cbf data/css/skeleton.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/css/skeleton.css Mon Jun 29 16:38:36 2015 +0100 |
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| 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 000000000000 -r ca58e9466cbf data/js/custom.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/js/custom.js Mon Jun 29 16:38:36 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() { + $("#overlay").hide(); + }); +} +); |
| b |
| diff -r 000000000000 -r ca58e9466cbf data/js/jquery-1.11.3.min.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/js/jquery-1.11.3.min.js Mon Jun 29 16:38:36 2015 +0100 |
| [ |
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| [ |
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| diff -r 000000000000 -r ca58e9466cbf data/js/jquery.tablesorter.min.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/js/jquery.tablesorter.min.js Mon Jun 29 16:38:36 2015 +0100 |
| [ |
| b'@@ -0,0 +1,4 @@\n+\n+(function($){$.extend({tablesorter:new\n+function(){var parsers=[],widgets=[];this.defaults={cssHeader:"header",cssAsc:"headerSortUp",cssDesc:"headerSortDown",cssChildRow:"expand-child",sortInitialOrder:"asc",sortMultiSortKey:"shiftKey",sortForce:null,sortAppend:null,sortLocaleCompare:true,textExtraction:"simple",parsers:{},widgets:[],widgetZebra:{css:["even","odd"]},headers:{},widthFixed:false,cancelSelection:true,sortList:[],headerList:[],dateFormat:"us",decimal:\'/\\.|\\,/g\',onRenderHeader:null,selectorHeaders:\'thead th\',debug:false};function benchmark(s,d){log(s+","+(new Date().getTime()-d.getTime())+"ms");}this.benchmark=benchmark;function log(s){if(typeof console!="undefined"&&typeof console.debug!="undefined"){console.log(s);}else{alert(s);}}function buildParserCache(table,$headers){if(table.config.debug){var parsersDebug="";}if(table.tBodies.length==0)return;var rows=table.tBodies[0].rows;if(rows[0]){var 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| b |
| diff -r 000000000000 -r ca58e9466cbf data/ribocount.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/ribocount.html Mon Jun 29 16:38:36 2015 +0100 |
| b |
| @@ -0,0 +1,64 @@ +<!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> + <p class="text-muted">Time taken for generating counts (H:MM:SS): {duration}</p> + </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> \ No newline at end of file |
| b |
| diff -r 000000000000 -r ca58e9466cbf data/ribocount_index.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/ribocount_index.html Mon Jun 29 16:38:36 2015 +0100 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r ca58e9466cbf data/riboplot.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/riboplot.html Mon Jun 29 16:38:36 2015 +0100 |
| b |
| @@ -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="ribograph.png"/><br> + <p> + <h4>Download plots<br> + <a href="ribograph.png">PNG</a>, <a href="ribograph.svg">SVG</a> + </h4> + + <h4>Download counts<br> + <a href="RiboCounts.csv">RiboCounts.csv</a> + </h4> + <p> + <small> + (Right click --> Save link/target as...) + </small> + </p> + </center> + </div> + </div> +</div> +</body> +</html> \ No newline at end of file |
| b |
| diff -r 000000000000 -r ca58e9466cbf ribocount.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribocount.xml Mon Jun 29 16:38:36 2015 +0100 |
| b |
| @@ -0,0 +1,31 @@ +<tool id="ribocount" name="ribocount" version="0.1.0"> + <description>Get read counts for all transcripts in an alignment (BAM) + </description> + <requirements> + <requirement type="package" version="0.7.7">pysam</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <command interpreter="python">./riboplot/ribocount.py + --ribo_file "${ribo_file}" + --transcriptome_fasta "${transcriptome_fasta}" + --read_length "${read_length}" + --read_offset "${read_offset}" + --html_file "${html_file}" + --output_path "${html_file.files_path}" + ## --debug + </command> + <inputs> + <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/> + <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/> + <param name="read_length" type="integer" label="Read length to consider" value="28"/> + <param name="read_offset" type="integer" label="Offset" value="0"/> + </inputs> + <outputs> + <data format="html" name="html_file" label="ribocount (HTML report)"/> + </outputs> + <help> + </help> +</tool> |
| b |
| diff -r 000000000000 -r ca58e9466cbf riboplot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot.xml Mon Jun 29 16:38:36 2015 +0100 |
| b |
| @@ -0,0 +1,54 @@ +<tool id="riboplot" name="riboplot" version="0.1.0"> + <description>Plot and output read counts for a single transcript in an alignment (BAM) + </description> + <requirements> + <requirement type="package" version="1.2.1">matplotlib</requirement> + <requirement type="package" version="0.7.7">pysam</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <command interpreter="python">./riboplot/riboplot.py + --ribo_file "${ribo_file}" + --transcriptome_fasta "${transcriptome_fasta}" + --transcript_name "${transcript_name}" + #if $rnacov.rnacov_select=="yes" + --rna_file "${rna_file}" + #end if + --read_length "${read_length}" + --read_offset "${read_offset}" + --html_file "${html_file}" + --output_path "${html_file.files_path}" + ## --debug + </command> + <inputs> + <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/> + <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/> + <param name="transcript_name" type="text" label="Name of the transcript to plot (as in FASTA)" size="40"> + <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator> + <validator type="empty_field" message="Field requires a value"/> + <sanitizer> + <valid> + <add value="|"/> + </valid> + </sanitizer> + </param> + <conditional name="rnacov"> + <param name="rnacov_select" type="select" label="Include RNA Coverage"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/> + </when> + </conditional> + <param name="read_length" type="integer" label="Read length to consider" value="28"/> + <param name="read_offset" type="integer" label="Offset" value="0"/> + </inputs> + <outputs> + <data format="html" name="html_file" label="riboplot (HTML report)"/> + </outputs> + <help> + </help> +</tool> |
| b |
| diff -r 000000000000 -r ca58e9466cbf riboplot/config.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/config.py Mon Jun 29 16:38:36 2015 +0100 |
| [ |
| @@ -0,0 +1,19 @@ +# -*- coding: utf-8 -*- +import os + + +class Config(object): + # get the running directory of this file, move one level up to get the + # application directory + APP_DIR = os.path.split(os.path.dirname(os.path.abspath(__file__)))[0] + + +class TestingConfig(Config): + """Testing configuration""" + 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') |
| b |
| diff -r 000000000000 -r ca58e9466cbf riboplot/core.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/core.py Mon Jun 29 16:38:36 2015 +0100 |
| [ |
| @@ -0,0 +1,66 @@ +"""Common functions. """ +import logging +import pysam + + +class BAMProfilesError(Exception): + pass + + +class BAMFileError(Exception): + pass + + +class TranscriptError(Exception): + pass + + +class RNACountsError(Exception): + """For errors related to RNA Coverage generation using bedtools. """ + pass + + +def check_bam_file(bam_file): + """Check if bam file is indexed. If not, index. """ + with pysam.AlignmentFile(bam_file, 'rb') as bam_fileobj: + try: + bam_fileobj.fetch(bam_fileobj.references[0]) + except ValueError as err: + if err.message == 'fetch called on bamfile without index': + bam_fileobj.close() + logging.debug('Indexing bam file {}'.format(bam_file)) + pysam.index(bam_file) + + +def get_ribo_counts(ribo_fileobj, transcript_name, read_length=None, read_offset=0): + """Get total reads and read counts in all 3 frames for the give transcript + from input BAM file (indexed). + + """ + read_counts = {} + total_reads = 0 + + if transcript_name not in ribo_fileobj.references: + raise BAMFileError('Transcript "{}" does not exist in BAM ' + 'file. '.format(transcript_name)) + + for record in ribo_fileobj.fetch(transcript_name): + if read_length: + if record.query_length != read_length: + continue + total_reads += 1 + position = record.pos + 1 + + try: + read_counts[position] + except KeyError: + read_counts[position] = {1: 0, 2: 0, 3: 0} + + rem = position % 3 + if rem == 0: + read_counts[position][3] += 1 + else: + read_counts[position][rem] += 1 + + return read_counts, total_reads + |
| b |
| diff -r 000000000000 -r ca58e9466cbf riboplot/ribocount.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/ribocount.py Mon Jun 29 16:38:36 2015 +0100 |
| [ |
| @@ -0,0 +1,150 @@ +# check dependencies +missing_deps = [] +try: + import pysam +except ImportError: + missing_deps.append('pysam') + +if len(missing_deps): + sys.exit('''\nCould not import the following modules. Please check if they + (or their dependencies are installed correctly. + \n\n{}\n'''.format('\n'.join(missing_deps))) + +import os +import sys +import timeit +import shutil +import zipfile +import logging +import argparse +from datetime import datetime + +import core +import config + +# Default is production +CONFIG = config.ProductionConfig() + + +def create_parser(): + """Argument parser. """ + parser = argparse.ArgumentParser( + prog='ribograph.counts', description='Output read counts for all transcripts') + + # required arguments + required = parser.add_argument_group('required arguments') + required.add_argument('--ribo_file', help='Ribo-Seq alignment file in BAM format', required=True) + required.add_argument('--transcriptome_fasta', help='FASTA format file of the transcriptome', required=True) + + # optional arguments + parser.add_argument('--read_length', help='Read length to consider (default: %(default)s)', + metavar='INTEGER', type=int) + parser.add_argument('--read_offset', help='Read offset (default: %(default)s)', + metavar='INTEGER', type=int, default=0) + parser.add_argument('--html_file', help='Output file for results (HTML)', default='ribocount.html') + parser.add_argument('--output_path', help='Files are saved in this directory', default='output') + parser.add_argument('--debug', help='Flag. Produce debug output', action='store_true') + + return parser + + +def main(): + parsed = create_parser() + args = parsed.parse_args() + + if args.debug: + level = logging.DEBUG + else: + level = logging.INFO + + logging.basicConfig(format='%(asctime)s: %(levelname)s %(message)s', + level=level, stream=sys.stdout, datefmt='%d/%m/%Y %I:%M:%S %p') + + start = datetime.now() + logging.debug('Start') + logging.debug('Supplied Arguments') + logging.debug('\n{}'.format('\n'.join(['{:<20}: {}'.format(k, v) for k, v in vars(args).items()]))) + + (ribo_file, transcriptome_fasta, read_length, read_offset) = ( + args.ribo_file, args.transcriptome_fasta, args.read_length, args.read_offset) + + logging.debug('Checking if BAM file is indexed') + core.check_bam_file(ribo_file) + + logging.debug('Get transcript information') + fasta_file = pysam.FastaFile(transcriptome_fasta) + + count = 0 + table_content = '' + + if not os.path.exists(args.output_path): + os.mkdir(args.output_path) + + output_path = os.path.join(args.output_path, 'ribocount_output') + if not os.path.exists(output_path): + os.mkdir(output_path) + + csv_dir = os.path.join(output_path, 'csv') + if not os.path.exists(csv_dir): + os.mkdir(csv_dir) + + bam_fileobj = pysam.AlignmentFile(ribo_file, 'rb') + for transcript in fasta_file.references: + rp_counts, rp_reads = core.get_ribo_counts(bam_fileobj, transcript, read_length, read_offset) + + if not rp_reads: + continue + + logging.debug('Writing counts for {}'.format(transcript)) + count += 1 + csv_file = 'RiboCounts{}.csv'.format(count) + with open(os.path.join(csv_dir, csv_file), 'w') as f: + f.write('"Position","Frame 1","Frame 2","Frame 3"\n') + + for pos in range(1, len(fasta_file[transcript]) + 1): + if pos in rp_counts: + f.write('{0},{1},{2},{3}\n'.format( + pos, rp_counts[pos][1], rp_counts[pos][2], rp_counts[pos][3])) + else: + f.write('{0},{1},{2},{3}\n'.format(pos, 0, 0, 0)) + if count % 2 == 0: + table_content += '<tr>' + else: + table_content += '<tr class="odd">' + table_content += '<td>{0}</td><td>{1}</td><td>{2}</td><td><a href="csv/{3}">{3}</a></td></tr>'.format( + count, transcript, rp_reads, csv_file) + bam_fileobj.close() + + if not read_length: + read_length = 'All' + + duration = str(datetime.now() - start).split('.')[0] + logging.debug('Time taken for generating counts {}'.format(duration)) + + with open(os.path.join(CONFIG.DATA_DIR, 'ribocount.html')) as g,\ + open(os.path.join(output_path, 'index.html'), 'w') as h: + h.write(g.read().format(count=count, length=read_length, table_content=table_content, duration=duration)) + + for asset in ('css', 'js'): + asset_dir = os.path.join(output_path, asset) + if not os.path.exists(asset_dir): + os.mkdir(asset_dir) + asset_data_dir = os.path.join(CONFIG.DATA_DIR, asset) + for fname in os.listdir(asset_data_dir): + shutil.copy(os.path.join(asset_data_dir, fname), + os.path.join(output_path, asset, fname)) + + logging.debug('Creating zip file') + os.chdir(args.output_path) + with zipfile.ZipFile('ribocount_output.zip', 'w') as zip: + for root, d, f in os.walk('ribocount_output'): + for name in f: + zip.write(os.path.join(root, name)) + + logging.debug('Writing HTML report') + + with open(os.path.join(CONFIG.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)) + +if __name__ == '__main__': + print timeit.timeit('main()', number=1, setup='from __main__ import main') |
| b |
| diff -r 000000000000 -r ca58e9466cbf riboplot/riboplot.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/riboplot/riboplot.py Mon Jun 29 16:38:36 2015 +0100 |
| [ |
| b'@@ -0,0 +1,319 @@\n+# check dependencies\n+missing_deps = []\n+try:\n+ import pysam\n+except ImportError:\n+ missing_deps.append(\'pysam\')\n+\n+try:\n+ from matplotlib import pyplot as plt\n+except ImportError:\n+ missing_deps.append(\'matplotlib\')\n+else:\n+ from matplotlib import gridspec\n+ from matplotlib.font_manager import FontProperties\n+\n+if len(missing_deps):\n+ sys.exit(\'\'\'\\nCould not import the following modules. Please check if they\n+ (or their dependencies are installed correctly.\n+ \\n\\n{}\\n\'\'\'.format(\'\\n\'.join(missing_deps)))\n+\n+\n+import os\n+import re\n+import sys\n+import config\n+import pysam\n+import timeit\n+import shutil\n+import logging\n+import tempfile\n+import argparse\n+import subprocess\n+\n+import core\n+# Default is production\n+CONFIG = config.ProductionConfig()\n+\n+\n+def get_start_stops(transcript_sequence, start_codons=None, stop_codons=None):\n+ """Return start and stop positions for all frames in the given\n+ transcript.\n+\n+ """\n+ if not start_codons:\n+ start_codons = [\'ATG\']\n+ if not stop_codons:\n+ stop_codons = [\'TAA\', \'TAG\', \'TGA\']\n+\n+ seq_frames = {1: {\'starts\': [], \'stops\': []},\n+ 2: {\'starts\': [], \'stops\': []},\n+ 3: {\'starts\': [], \'stops\': []}}\n+\n+ for codons, positions in ((start_codons, \'starts\'),\n+ (stop_codons, \'stops\')):\n+ if len(codons) > 1:\n+ pat = re.compile(\'|\'.join(codons))\n+ else:\n+ pat = re.compile(codons[0])\n+\n+ for m in re.finditer(pat, transcript_sequence):\n+ # Increment position by 1, Frame 1 starts at position 1 not 0\n+ start = m.start() + 1\n+ rem = start % 3\n+ if rem == 1: # frame 1\n+ seq_frames[1][positions].append(start)\n+ elif rem == 2: # frame 2\n+ seq_frames[2][positions].append(start)\n+ elif rem == 0: # frame 3\n+ seq_frames[3][positions].append(start)\n+ return seq_frames\n+\n+\n+def get_rna_counts(rna_file, transcript_name):\n+ """Get coverage for a given RNA BAM file, return read counts. """\n+ try:\n+ subprocess.check_output([\'bedtools\', \'--version\'])\n+ except OSError:\n+ logging.error(\'Could not find bedtools in PATH. bedtools is \'\n+ \'required for generating RNA coverage plot. \')\n+ raise\n+ logging.debug(\'Get RNA coverage for transcript using bedtools\')\n+ # check if the RNA file exists\n+ if not os.path.exists(rna_file):\n+ msg = \'RNA-Seq BAM file "{}" does not exist\'.format(rna_file)\n+ logging.error(msg)\n+ raise OSError(msg)\n+ rna_counts = {}\n+\n+ cov_file = tempfile.NamedTemporaryFile(delete=False)\n+ try:\n+ subprocess.check_call(\n+ [\'bedtools\', \'genomecov\', \'-ibam\', rna_file,\n+ \'-bg\'], stdout=cov_file)\n+ except subprocess.CalledProcessError as e:\n+ # needs testing\n+ raise core.RNACountsError(\'Could not generate coverage for RNA BAM file. \\n{}\\n\'.format(e))\n+ logging.debug(\'Finished generating RNA coverage\')\n+ logging.debug(\'Processing coverage file\')\n+ for line in open(cov_file.name):\n+ line = line.split()\n+ if line[0] == transcript_name:\n+ position, count = int(line[1]) + 1, int(line[3])\n+ rna_counts[position] = count\n+ cov_file.close()\n+ os.unlink(cov_file.name)\n+ logging.debug(\'Finished processing coverage file\')\n+ return rna_counts\n+\n+\n+def plot_profile(ribo_counts, transcript_name, transcript_length,\n+ start_stops, read_length=None, read_offset=None, rna_counts=None,\n+ html_file=\'index.html\', output_path=\'output\'):\n+ """Plot read counts (in all 3 frames) and RNA coverage if provided for a\n+ single transcript.\n+\n+ """\n+ gs = gridspec.GridSpec(4, 1, height_ratios=[7, 1, 1, 1])\n+ '..b't file in BAM format\', required=True)\n+ required.add_argument(\'--transcriptome_fasta\', help=\'FASTA format file of the transcriptome\', required=True)\n+ required.add_argument(\'--transcript_name\', help=\'Transcript name\', metavar=\'TEXT\', required=True)\n+\n+ # plot function - optional arguments\n+ parser.add_argument(\'--rna_file\', help=\'RNA-Seq alignment file (BAM)\')\n+ parser.add_argument(\'--read_length\', help=\'Read length to consider (default: %(default)s)\',\n+ metavar=\'INTEGER\', type=int)\n+ parser.add_argument(\'--read_offset\', help=\'Read offset (default: %(default)s)\',\n+ metavar=\'INTEGER\', type=int, default=0)\n+ parser.add_argument(\'--html_file\', help=\'Output file for results (HTML)\', default=\'index.html\')\n+ parser.add_argument(\'--output_path\', help=\'Files are saved in this directory\', default=\'output\')\n+ parser.add_argument(\'--debug\', help=\'Flag. Produce debug output\', action=\'store_true\')\n+\n+ return parser\n+\n+\n+def main():\n+ """Start program. """\n+ parsed = create_parser()\n+ args = parsed.parse_args()\n+\n+ if args.debug:\n+ level = logging.DEBUG\n+ else:\n+ level = logging.INFO\n+\n+ logging.basicConfig(format=\'%(asctime)s: %(levelname)s %(message)s\',\n+ level=level, stream=sys.stdout, datefmt=\'%d/%m/%Y %I:%M:%S %p\')\n+\n+ logging.debug(\'Start\')\n+ logging.debug(\'Supplied Arguments\')\n+ logging.debug(\'\\n{}\'.format(\'\\n\'.join([\'{:<20}: {}\'.format(k, v) for k, v in vars(args).items()])))\n+\n+ (ribo_file, rna_file, transcript_name, transcriptome_fasta, read_length,\n+ read_offset, output_path) = (args.ribo_file, args.rna_file, args.transcript_name,\n+ args.transcriptome_fasta, args.read_length, args.read_offset, args.output_path)\n+\n+ logging.debug(\'Checking if BAM file is indexed...\')\n+ core.check_bam_file(ribo_file)\n+\n+ logging.debug(\'Get transcript information...\')\n+ transcripts = pysam.FastaFile(transcriptome_fasta)\n+ sequence = transcripts.fetch(transcript_name)\n+ length = len(sequence)\n+\n+ if not length:\n+ logging.error(\'Transcript "{}" does not exist in transcriptome \'\n+ \'FASTA file "{}"\'.format(transcript_name, os.path.basename(transcriptome_fasta)))\n+ sys.exit(1)\n+\n+ logging.debug(\'Get start/stop positions in transcript (3 frames)...\')\n+ codon_positions = get_start_stops(sequence)\n+\n+ mrna_counts = {}\n+ if rna_file:\n+ try:\n+ mrna_counts = get_rna_counts(rna_file, transcript_name)\n+ except OSError as e:\n+ sys.exit(e)\n+ else:\n+ logging.debug(\'No RNA-Seq data provided. Not generating coverage\')\n+\n+ logging.debug(\'Get ribo-seq read counts and total reads in Ribo-Seq...\')\n+ bam_fileobj = pysam.AlignmentFile(ribo_file, \'rb\')\n+ ribo_counts, total_reads = core.get_ribo_counts(bam_fileobj, transcript_name, read_length, read_offset)\n+ bam_fileobj.close()\n+\n+ if not os.path.exists(output_path):\n+ os.mkdir(output_path)\n+\n+ logging.debug(\'Writing counts for {}\'.format(transcript_name))\n+ with open(os.path.join(output_path, \'RiboCounts.csv\'), \'w\') as f:\n+ f.write(\'"Position","Frame 1","Frame 2","Frame 3"\\n\')\n+\n+ for pos in range(1, length + 1):\n+ if pos in ribo_counts:\n+ f.write(\'{0},{1},{2},{3}\\n\'.format(\n+ pos, ribo_counts[pos][1], ribo_counts[pos][2], ribo_counts[pos][3]))\n+ else:\n+ f.write(\'{0},{1},{2},{3}\\n\'.format(pos, 0, 0, 0))\n+\n+ logging.debug(\'Generating plot...\')\n+ plot_profile(ribo_counts, transcript_name, length,\n+ codon_positions, read_length, read_offset, mrna_counts,\n+ html_file=os.path.join(args.output_path, args.html_file),\n+ output_path=args.output_path)\n+ logging.debug(\'Finished\')\n+\n+\n+if __name__ == \'__main__\':\n+ print timeit.timeit(\'main()\', number=1, setup=\'from __main__ import main\')\n' |
| b |
| diff -r 000000000000 -r ca58e9466cbf runtests.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runtests.sh Mon Jun 29 16:38:36 2015 +0100 |
| b |
| @@ -0,0 +1,2 @@ +#!/bin/bash +python -m unittest discover --verbose |
| b |
| diff -r 000000000000 -r ca58e9466cbf tests/test_plot.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/test_plot.py Mon Jun 29 16:38:36 2015 +0100 |
| [ |
| @@ -0,0 +1,52 @@ +import os +import logging +import unittest + +from riboplot import core, config, plot + +# use testing configuration +CONFIG = plot.CONFIG = 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') +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') + +class RNACountsTestCase(unittest.TestCase): + + def test_get_rna_counts(self): + """Test get RNA counts for transcript from RNA-Seq BAM file""" + counts = plot.get_rna_counts(rna_file=RNA_FILE, transcript_name=TRANSCRIPT_NAME) + self.assertIsInstance(counts, dict) + self.assertTrue(len(counts) > 0) + + def test_missing_rna_file(self): + """Exit with error if RNA BAM file does not exist. """ + self.assertRaises(OSError, plot.get_rna_counts, rna_file='{}.absent'.format(RNA_FILE), + transcript_name=TRANSCRIPT_NAME) + + def test_missing_bedtools(self): + """Exit with error if bedtools is missing.""" + # reset env temporarily + paths = os.environ['PATH'] + os.environ['PATH'] = '' + self.assertRaises(OSError, plot.get_rna_counts, rna_file=RNA_FILE, + transcript_name=TRANSCRIPT_NAME) + os.environ['PATH'] = paths + + +class PlotTestCase(unittest.TestCase): + + def test_get_codon_positions(self): + """Test get codon positions. """ + # input is the sequence obtained from get_transcript so no new lines. + fasta = ('AACCGGAGCACCCAGAGAAAACCCACGCAAACGCAGGGAGAATTTGCAAACTCCACACA' + 'GAAATGCCAGCTGATCCAGCCGAGCCTCGAGTCAGCATCCTTGCTTGTTGGATGCCTGA' + 'TTGCAGTTCAACTCCAAACTCAGTTGGACCAGCTGATCAGTG') + codon_positions = plot.get_start_stops(fasta) + expected = {1: {'starts': [], 'stops': []}, + 2: {'starts': [], 'stops': [71, 116, 152]}, + 3: {'starts': [63, 111], 'stops': []}} + self.assertEqual(codon_positions, expected) \ No newline at end of file |
| b |
| diff -r 000000000000 -r ca58e9466cbf tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jun 29 16:38:36 2015 +0100 |
| b |
| @@ -0,0 +1,18 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="matplotlib" version="1.2.1"> + <repository changeset_revision="d22042e5e279" name="package_matplotlib_1_2" + owner="ribogalaxy" prior_installation_required="True" + toolshed="http://toolshed.ribogalaxy.ucc.ie" /> + </package> + <package name="pysam" version="0.7.7"> + <repository changeset_revision="0e8f87bbc1e8" name="package_pysam_0_7_7" + owner="ribogalaxy" prior_installation_required="True" + toolshed="http://toolshed.ribogalaxy.ucc.ie" /> + </package> + <package name="samtools" version="0.1.18"> + <repository changeset_revision="4407d444b269" name="package_samtools_0_1_18" + owner="ribogalaxy" prior_installation_required="True" + toolshed="http://toolshed.ribogalaxy.ucc.ie" /> + </package> +</tool_dependency> |
