Nantes Université

Skip to content
Extraits de code Groupes Projets
Valider 38cb9ebc rédigé par adrien's avatar adrien
Parcourir les fichiers

Create gh-pages branch via GitHub

parent
Aucune branche associée trouvée
Aucune étiquette associée trouvée
Aucune requête de fusion associée trouvée
<!DOCTYPE html>
<html lang="en-us">
<head>
<meta charset="UTF-8">
<title>Pyfastq by a-slide</title>
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" type="text/css" href="stylesheets/normalize.css" media="screen">
<link href='http://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>
<link rel="stylesheet" type="text/css" href="stylesheets/stylesheet.css" media="screen">
<link rel="stylesheet" type="text/css" href="stylesheets/github-light.css" media="screen">
</head>
<body>
<section class="page-header">
<h1 class="project-name">Pyfastq</h1>
<h2 class="project-tagline">Simple python 2.7 libraries to parse fastq files and handle fastq sequences</h2>
<a href="https://github.com/a-slide/pyFastq" class="btn">View on GitHub</a>
<a href="https://github.com/a-slide/pyFastq/zipball/master" class="btn">Download .zip</a>
<a href="https://github.com/a-slide/pyFastq/tarball/master" class="btn">Download .tar.gz</a>
</section>
<section class="main-content">
<h1>
<a id="pyfastq-01" class="anchor" href="#pyfastq-01" aria-hidden="true"><span class="octicon octicon-link"></span></a>pyFastq 0.1</h1>
<p><strong>Simple python 2.7 libraries to parse fastq files and handle illumina 1.8+ fastq sequences</strong></p>
<p><strong>Creation : 2015/04/02</strong></p>
<p><strong>Last update : 2015/04/02</strong></p>
<h2>
<a id="fastqreader" class="anchor" href="#fastqreader" aria-hidden="true"><span class="octicon octicon-link"></span></a>FastqReader</h2>
<p>Parsing function that reads a fastq file and generates an iterator of FastqSeq object.
When the file is empty the generator raise a StopIteration exception indicating the number of valid sequence parsed. If a fastq sequence is invalid, this sequence is skipped.
Any part of the sequence name following a blank space will be removed</p>
<h2>
<a id="fastqseq--simple-object-representing-a-fastq-sequence" class="anchor" href="#fastqseq--simple-object-representing-a-fastq-sequence" aria-hidden="true"><span class="octicon octicon-link"></span></a>FastqSeq : Simple object representing a Fastq sequence</h2>
<p>FastqSeq is a simple python object class generating a object representing a Fastq sequence. The object is initialized with:</p>
<ul>
<li>A name for the sequence without @</li>
<li>A DNA sequence as a string</li>
<li>A quality score, as an <strong>illumina 1.8+</strong> encoded quality string, a numpy.ndarray of integers in <strong>Phred +33</strong> or python list of integers in <strong>Phred +33</strong>
</li>
<li>Eventually a short text description</li>
</ul>
<p>The DNA sequence and the quality score must have the same size otherwise an assertion error is raised</p>
<p>After creation the object has the following fields:</p>
<ul>
<li>name = name of the sequence without @.</li>
<li>seq = The DNA sequence of the fastq sequence store as a simple string.</li>
<li>qual = An numpy integer ndarray representing the Phred Quality of bases (support all np.array methods)</li>
<li>descr = A description of the fastq sequence.</li>
<li>qualstr = A string of letters corresponding to the sequence quality in illumina 1.8+ Phred 33 encoding</li>
<li>fastqstr = The field "descr" will be included in the output fastq sequence name after a space if present</li>
</ul>
<p>The object support slicing([0:10]), concatenation(seq1+seq2) and the len method</p>
<h2>
<a id="authors-and-contact" class="anchor" href="#authors-and-contact" aria-hidden="true"><span class="octicon octicon-link"></span></a>Authors and Contact</h2>
<p>Adrien Leger - 2015</p>
<ul>
<li>
<a href="mailto:adrien.leger@gmail.com">adrien.leger@gmail.com</a> - <a href="mailto:adrien.leger@inserm.fr">adrien.leger@inserm.fr</a> - <a href="mailto:adrien.leger@univ-nantes.fr">adrien.leger@univ-nantes.fr</a>
</li>
<li><a href="https://github.com/a-slide">Github</a></li>
<li><a href="http://www.atlantic-gene-therapies.fr/">Atlantic Gene Therapies - INSERM 1089</a></li>
</ul>
<footer class="site-footer">
<span class="site-footer-owner"><a href="https://github.com/a-slide/pyFastq">Pyfastq</a> is maintained by <a href="https://github.com/a-slide">a-slide</a>.</span>
<span class="site-footer-credits">This page was generated by <a href="https://pages.github.com">GitHub Pages</a> using the <a href="https://github.com/jasonlong/cayman-theme">Cayman theme</a> by <a href="https://twitter.com/jasonlong">Jason Long</a>.</span>
</footer>
</section>
</body>
</html>
{"name":"Pyfastq","tagline":"Simple python 2.7 libraries to parse fastq files and handle fastq sequences","body":"# pyFastq 0.1\r\n\r\n**Simple python 2.7 libraries to parse fastq files and handle illumina 1.8+ fastq sequences**\r\n\r\n**Creation : 2015/04/02**\r\n\r\n**Last update : 2015/04/02**\r\n\r\n## FastqReader\r\nParsing function that reads a fastq file and generates an iterator of FastqSeq object.\r\nWhen the file is empty the generator raise a StopIteration exception indicating the number of valid sequence parsed. If a fastq sequence is invalid, this sequence is skipped.\r\nAny part of the sequence name following a blank space will be removed\r\n\r\n## FastqSeq : Simple object representing a Fastq sequence\r\nFastqSeq is a simple python object class generating a object representing a Fastq sequence. The object is initialized with:\r\n\r\n* A name for the sequence without @\r\n* A DNA sequence as a string\r\n* A quality score, as an **illumina 1.8+** encoded quality string, a numpy.ndarray of integers in **Phred +33** or python list of integers in **Phred +33**\r\n* Eventually a short text description\r\n\r\nThe DNA sequence and the quality score must have the same size otherwise an assertion error is raised\r\n\r\nAfter creation the object has the following fields:\r\n\r\n* name = name of the sequence without @.\r\n* seq = The DNA sequence of the fastq sequence store as a simple string.\r\n* qual = An numpy integer ndarray representing the Phred Quality of bases (support all np.array methods)\r\n* descr = A description of the fastq sequence.\r\n* qualstr = A string of letters corresponding to the sequence quality in illumina 1.8+ Phred 33 encoding\r\n* fastqstr = The field \"descr\" will be included in the output fastq sequence name after a space if present\r\n\r\nThe object support slicing([0:10]), concatenation(seq1+seq2) and the len method\r\n\r\n## Authors and Contact\r\n\r\nAdrien Leger - 2015\r\n\r\n* <adrien.leger@gmail.com> - <adrien.leger@inserm.fr> - <adrien.leger@univ-nantes.fr>\r\n* [Github](https://github.com/a-slide)\r\n* [Atlantic Gene Therapies - INSERM 1089](http://www.atlantic-gene-therapies.fr/)\r\n","google":"","note":"Don't delete this file! It's used internally to help with page regeneration."}
\ No newline at end of file
/*
Copyright 2014 GitHub Inc.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
*/
.pl-c /* comment */ {
color: #969896;
}
.pl-c1 /* constant, markup.raw, meta.diff.header, meta.module-reference, meta.property-name, support, support.constant, support.variable, variable.other.constant */,
.pl-s .pl-v /* string variable */ {
color: #0086b3;
}
.pl-e /* entity */,
.pl-en /* entity.name */ {
color: #795da3;
}
.pl-s .pl-s1 /* string source */,
.pl-smi /* storage.modifier.import, storage.modifier.package, storage.type.java, variable.other, variable.parameter.function */ {
color: #333;
}
.pl-ent /* entity.name.tag */ {
color: #63a35c;
}
.pl-k /* keyword, storage, storage.type */ {
color: #a71d5d;
}
.pl-pds /* punctuation.definition.string, string.regexp.character-class */,
.pl-s /* string */,
.pl-s .pl-pse .pl-s1 /* string punctuation.section.embedded source */,
.pl-sr /* string.regexp */,
.pl-sr .pl-cce /* string.regexp constant.character.escape */,
.pl-sr .pl-sra /* string.regexp string.regexp.arbitrary-repitition */,
.pl-sr .pl-sre /* string.regexp source.ruby.embedded */ {
color: #183691;
}
.pl-v /* variable */ {
color: #ed6a43;
}
.pl-id /* invalid.deprecated */ {
color: #b52a1d;
}
.pl-ii /* invalid.illegal */ {
background-color: #b52a1d;
color: #f8f8f8;
}
.pl-sr .pl-cce /* string.regexp constant.character.escape */ {
color: #63a35c;
font-weight: bold;
}
.pl-ml /* markup.list */ {
color: #693a17;
}
.pl-mh /* markup.heading */,
.pl-mh .pl-en /* markup.heading entity.name */,
.pl-ms /* meta.separator */ {
color: #1d3e81;
font-weight: bold;
}
.pl-mq /* markup.quote */ {
color: #008080;
}
.pl-mi /* markup.italic */ {
color: #333;
font-style: italic;
}
.pl-mb /* markup.bold */ {
color: #333;
font-weight: bold;
}
.pl-md /* markup.deleted, meta.diff.header.from-file */ {
background-color: #ffecec;
color: #bd2c00;
}
.pl-mi1 /* markup.inserted, meta.diff.header.to-file */ {
background-color: #eaffea;
color: #55a532;
}
.pl-mdr /* meta.diff.range */ {
color: #795da3;
font-weight: bold;
}
.pl-mo /* meta.output */ {
color: #1d3e81;
}
/*! normalize.css v3.0.2 | MIT License | git.io/normalize */
/**
* 1. Set default font family to sans-serif.
* 2. Prevent iOS text size adjust after orientation change, without disabling
* user zoom.
*/
html {
font-family: sans-serif; /* 1 */
-ms-text-size-adjust: 100%; /* 2 */
-webkit-text-size-adjust: 100%; /* 2 */
}
/**
* Remove default margin.
*/
body {
margin: 0;
}
/* HTML5 display definitions
========================================================================== */
/**
* Correct `block` display not defined for any HTML5 element in IE 8/9.
* Correct `block` display not defined for `details` or `summary` in IE 10/11
* and Firefox.
* Correct `block` display not defined for `main` in IE 11.
*/
article,
aside,
details,
figcaption,
figure,
footer,
header,
hgroup,
main,
menu,
nav,
section,
summary {
display: block;
}
/**
* 1. Correct `inline-block` display not defined in IE 8/9.
* 2. Normalize vertical alignment of `progress` in Chrome, Firefox, and Opera.
*/
audio,
canvas,
progress,
video {
display: inline-block; /* 1 */
vertical-align: baseline; /* 2 */
}
/**
* Prevent modern browsers from displaying `audio` without controls.
* Remove excess height in iOS 5 devices.
*/
audio:not([controls]) {
display: none;
height: 0;
}
/**
* Address `[hidden]` styling not present in IE 8/9/10.
* Hide the `template` element in IE 8/9/11, Safari, and Firefox < 22.
*/
[hidden],
template {
display: none;
}
/* Links
========================================================================== */
/**
* Remove the gray background color from active links in IE 10.
*/
a {
background-color: transparent;
}
/**
* Improve readability when focused and also mouse hovered in all browsers.
*/
a:active,
a:hover {
outline: 0;
}
/* Text-level semantics
========================================================================== */
/**
* Address styling not present in IE 8/9/10/11, Safari, and Chrome.
*/
abbr[title] {
border-bottom: 1px dotted;
}
/**
* Address style set to `bolder` in Firefox 4+, Safari, and Chrome.
*/
b,
strong {
font-weight: bold;
}
/**
* Address styling not present in Safari and Chrome.
*/
dfn {
font-style: italic;
}
/**
* Address variable `h1` font-size and margin within `section` and `article`
* contexts in Firefox 4+, Safari, and Chrome.
*/
h1 {
font-size: 2em;
margin: 0.67em 0;
}
/**
* Address styling not present in IE 8/9.
*/
mark {
background: #ff0;
color: #000;
}
/**
* Address inconsistent and variable font size in all browsers.
*/
small {
font-size: 80%;
}
/**
* Prevent `sub` and `sup` affecting `line-height` in all browsers.
*/
sub,
sup {
font-size: 75%;
line-height: 0;
position: relative;
vertical-align: baseline;
}
sup {
top: -0.5em;
}
sub {
bottom: -0.25em;
}
/* Embedded content
========================================================================== */
/**
* Remove border when inside `a` element in IE 8/9/10.
*/
img {
border: 0;
}
/**
* Correct overflow not hidden in IE 9/10/11.
*/
svg:not(:root) {
overflow: hidden;
}
/* Grouping content
========================================================================== */
/**
* Address margin not present in IE 8/9 and Safari.
*/
figure {
margin: 1em 40px;
}
/**
* Address differences between Firefox and other browsers.
*/
hr {
box-sizing: content-box;
height: 0;
}
/**
* Contain overflow in all browsers.
*/
pre {
overflow: auto;
}
/**
* Address odd `em`-unit font size rendering in all browsers.
*/
code,
kbd,
pre,
samp {
font-family: monospace, monospace;
font-size: 1em;
}
/* Forms
========================================================================== */
/**
* Known limitation: by default, Chrome and Safari on OS X allow very limited
* styling of `select`, unless a `border` property is set.
*/
/**
* 1. Correct color not being inherited.
* Known issue: affects color of disabled elements.
* 2. Correct font properties not being inherited.
* 3. Address margins set differently in Firefox 4+, Safari, and Chrome.
*/
button,
input,
optgroup,
select,
textarea {
color: inherit; /* 1 */
font: inherit; /* 2 */
margin: 0; /* 3 */
}
/**
* Address `overflow` set to `hidden` in IE 8/9/10/11.
*/
button {
overflow: visible;
}
/**
* Address inconsistent `text-transform` inheritance for `button` and `select`.
* All other form control elements do not inherit `text-transform` values.
* Correct `button` style inheritance in Firefox, IE 8/9/10/11, and Opera.
* Correct `select` style inheritance in Firefox.
*/
button,
select {
text-transform: none;
}
/**
* 1. Avoid the WebKit bug in Android 4.0.* where (2) destroys native `audio`
* and `video` controls.
* 2. Correct inability to style clickable `input` types in iOS.
* 3. Improve usability and consistency of cursor style between image-type
* `input` and others.
*/
button,
html input[type="button"], /* 1 */
input[type="reset"],
input[type="submit"] {
-webkit-appearance: button; /* 2 */
cursor: pointer; /* 3 */
}
/**
* Re-set default cursor for disabled elements.
*/
button[disabled],
html input[disabled] {
cursor: default;
}
/**
* Remove inner padding and border in Firefox 4+.
*/
button::-moz-focus-inner,
input::-moz-focus-inner {
border: 0;
padding: 0;
}
/**
* Address Firefox 4+ setting `line-height` on `input` using `!important` in
* the UA stylesheet.
*/
input {
line-height: normal;
}
/**
* It's recommended that you don't attempt to style these elements.
* Firefox's implementation doesn't respect box-sizing, padding, or width.
*
* 1. Address box sizing set to `content-box` in IE 8/9/10.
* 2. Remove excess padding in IE 8/9/10.
*/
input[type="checkbox"],
input[type="radio"] {
box-sizing: border-box; /* 1 */
padding: 0; /* 2 */
}
/**
* Fix the cursor style for Chrome's increment/decrement buttons. For certain
* `font-size` values of the `input`, it causes the cursor style of the
* decrement button to change from `default` to `text`.
*/
input[type="number"]::-webkit-inner-spin-button,
input[type="number"]::-webkit-outer-spin-button {
height: auto;
}
/**
* 1. Address `appearance` set to `searchfield` in Safari and Chrome.
* 2. Address `box-sizing` set to `border-box` in Safari and Chrome
* (include `-moz` to future-proof).
*/
input[type="search"] {
-webkit-appearance: textfield; /* 1 */ /* 2 */
box-sizing: content-box;
}
/**
* Remove inner padding and search cancel button in Safari and Chrome on OS X.
* Safari (but not Chrome) clips the cancel button when the search input has
* padding (and `textfield` appearance).
*/
input[type="search"]::-webkit-search-cancel-button,
input[type="search"]::-webkit-search-decoration {
-webkit-appearance: none;
}
/**
* Define consistent border, margin, and padding.
*/
fieldset {
border: 1px solid #c0c0c0;
margin: 0 2px;
padding: 0.35em 0.625em 0.75em;
}
/**
* 1. Correct `color` not being inherited in IE 8/9/10/11.
* 2. Remove padding so people aren't caught out if they zero out fieldsets.
*/
legend {
border: 0; /* 1 */
padding: 0; /* 2 */
}
/**
* Remove default vertical scrollbar in IE 8/9/10/11.
*/
textarea {
overflow: auto;
}
/**
* Don't inherit the `font-weight` (applied by a rule above).
* NOTE: the default cannot safely be changed in Chrome and Safari on OS X.
*/
optgroup {
font-weight: bold;
}
/* Tables
========================================================================== */
/**
* Remove most spacing between table cells.
*/
table {
border-collapse: collapse;
border-spacing: 0;
}
td,
th {
padding: 0;
}
* {
box-sizing: border-box; }
body {
padding: 0;
margin: 0;
font-family: "Open Sans", "Helvetica Neue", Helvetica, Arial, sans-serif;
font-size: 16px;
line-height: 1.5;
color: #606c71; }
a {
color: #1e6bb8;
text-decoration: none; }
a:hover {
text-decoration: underline; }
.btn {
display: inline-block;
margin-bottom: 1rem;
color: rgba(255, 255, 255, 0.7);
background-color: rgba(255, 255, 255, 0.08);
border-color: rgba(255, 255, 255, 0.2);
border-style: solid;
border-width: 1px;
border-radius: 0.3rem;
transition: color 0.2s, background-color 0.2s, border-color 0.2s; }
.btn + .btn {
margin-left: 1rem; }
.btn:hover {
color: rgba(255, 255, 255, 0.8);
text-decoration: none;
background-color: rgba(255, 255, 255, 0.2);
border-color: rgba(255, 255, 255, 0.3); }
@media screen and (min-width: 64em) {
.btn {
padding: 0.75rem 1rem; } }
@media screen and (min-width: 42em) and (max-width: 64em) {
.btn {
padding: 0.6rem 0.9rem;
font-size: 0.9rem; } }
@media screen and (max-width: 42em) {
.btn {
display: block;
width: 100%;
padding: 0.75rem;
font-size: 0.9rem; }
.btn + .btn {
margin-top: 1rem;
margin-left: 0; } }
.page-header {
color: #fff;
text-align: center;
background-color: #159957;
background-image: linear-gradient(120deg, #155799, #159957); }
@media screen and (min-width: 64em) {
.page-header {
padding: 5rem 6rem; } }
@media screen and (min-width: 42em) and (max-width: 64em) {
.page-header {
padding: 3rem 4rem; } }
@media screen and (max-width: 42em) {
.page-header {
padding: 2rem 1rem; } }
.project-name {
margin-top: 0;
margin-bottom: 0.1rem; }
@media screen and (min-width: 64em) {
.project-name {
font-size: 3.25rem; } }
@media screen and (min-width: 42em) and (max-width: 64em) {
.project-name {
font-size: 2.25rem; } }
@media screen and (max-width: 42em) {
.project-name {
font-size: 1.75rem; } }
.project-tagline {
margin-bottom: 2rem;
font-weight: normal;
opacity: 0.7; }
@media screen and (min-width: 64em) {
.project-tagline {
font-size: 1.25rem; } }
@media screen and (min-width: 42em) and (max-width: 64em) {
.project-tagline {
font-size: 1.15rem; } }
@media screen and (max-width: 42em) {
.project-tagline {
font-size: 1rem; } }
.main-content :first-child {
margin-top: 0; }
.main-content img {
max-width: 100%; }
.main-content h1, .main-content h2, .main-content h3, .main-content h4, .main-content h5, .main-content h6 {
margin-top: 2rem;
margin-bottom: 1rem;
font-weight: normal;
color: #159957; }
.main-content p {
margin-bottom: 1em; }
.main-content code {
padding: 2px 4px;
font-family: Consolas, "Liberation Mono", Menlo, Courier, monospace;
font-size: 0.9rem;
color: #383e41;
background-color: #f3f6fa;
border-radius: 0.3rem; }
.main-content pre {
padding: 0.8rem;
margin-top: 0;
margin-bottom: 1rem;
font: 1rem Consolas, "Liberation Mono", Menlo, Courier, monospace;
color: #567482;
word-wrap: normal;
background-color: #f3f6fa;
border: solid 1px #dce6f0;
border-radius: 0.3rem; }
.main-content pre > code {
padding: 0;
margin: 0;
font-size: 0.9rem;
color: #567482;
word-break: normal;
white-space: pre;
background: transparent;
border: 0; }
.main-content .highlight {
margin-bottom: 1rem; }
.main-content .highlight pre {
margin-bottom: 0;
word-break: normal; }
.main-content .highlight pre, .main-content pre {
padding: 0.8rem;
overflow: auto;
font-size: 0.9rem;
line-height: 1.45;
border-radius: 0.3rem; }
.main-content pre code, .main-content pre tt {
display: inline;
max-width: initial;
padding: 0;
margin: 0;
overflow: initial;
line-height: inherit;
word-wrap: normal;
background-color: transparent;
border: 0; }
.main-content pre code:before, .main-content pre code:after, .main-content pre tt:before, .main-content pre tt:after {
content: normal; }
.main-content ul, .main-content ol {
margin-top: 0; }
.main-content blockquote {
padding: 0 1rem;
margin-left: 0;
color: #819198;
border-left: 0.3rem solid #dce6f0; }
.main-content blockquote > :first-child {
margin-top: 0; }
.main-content blockquote > :last-child {
margin-bottom: 0; }
.main-content table {
display: block;
width: 100%;
overflow: auto;
word-break: normal;
word-break: keep-all; }
.main-content table th {
font-weight: bold; }
.main-content table th, .main-content table td {
padding: 0.5rem 1rem;
border: 1px solid #e9ebec; }
.main-content dl {
padding: 0; }
.main-content dl dt {
padding: 0;
margin-top: 1rem;
font-size: 1rem;
font-weight: bold; }
.main-content dl dd {
padding: 0;
margin-bottom: 1rem; }
.main-content hr {
height: 2px;
padding: 0;
margin: 1rem 0;
background-color: #eff0f1;
border: 0; }
@media screen and (min-width: 64em) {
.main-content {
max-width: 64rem;
padding: 2rem 6rem;
margin: 0 auto;
font-size: 1.1rem; } }
@media screen and (min-width: 42em) and (max-width: 64em) {
.main-content {
padding: 2rem 4rem;
font-size: 1.1rem; } }
@media screen and (max-width: 42em) {
.main-content {
padding: 2rem 1rem;
font-size: 1rem; } }
.site-footer {
padding-top: 2rem;
margin-top: 2rem;
border-top: solid 1px #eff0f1; }
.site-footer-owner {
display: block;
font-weight: bold; }
.site-footer-credits {
color: #819198; }
@media screen and (min-width: 64em) {
.site-footer {
font-size: 1rem; } }
@media screen and (min-width: 42em) and (max-width: 64em) {
.site-footer {
font-size: 1rem; } }
@media screen and (max-width: 42em) {
.site-footer {
font-size: 0.9rem; } }
0% Chargement en cours ou .
You are about to add 0 people to the discussion. Proceed with caution.
Terminez d'abord l'édition de ce message.
Veuillez vous inscrire ou vous pour commenter