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# Sphinx build info version 1 | ||
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. | ||
config: 68666ed7422b1e0bf84ee532afdab9b6 | ||
tags: 645f666f9bcd5a90fca523b33c5a78b7 |
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HogProf | ||
===================== | ||
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- HogProf is an extensible and tunable approach to phylogenetic profiling using orthology data. It is powered by minhash based datastructures and computationally efficient. | ||
- Still under major development and may change. | ||
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.. toctree:: | ||
:maxdepth: 2 | ||
:caption: Contents: | ||
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installation | ||
usage | ||
troubleshooting | ||
credits | ||
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Installation | ||
------------ | ||
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To install My Project, run the following command: | ||
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Using pip | ||
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.. code-block:: bash | ||
$ pip install hogprof | ||
Or from github | ||
.. code-block:: bash | ||
$ git clone https://github.com/DessimozLab/HogProf.git | ||
$ pip install -r pipreqs.txt . | ||
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Quickstart | ||
----- | ||
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To use the library we need an OMA instance's HDF5 file containing HOG info and some accesory files. | ||
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.. code-block:: bash | ||
$ mkdir YourOmaDirectory | ||
$ cd YourOmaDirectory | ||
$ wget https://omabrowser.org/All/OmaServer.h5 | ||
$ wget https://omabrowser.org/All/oma-go.txt.gz | ||
Let's create a directory for the phylogenetic rpfiling database were going to make. | ||
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.. code-block:: bash | ||
$ mkdir YourDBDirectory | ||
Ok. We're ready! Now let's compile a database containing all HOGs and our desired taxonomic levels using default settings. Launch the lshbuilder. | ||
dbtypes available on the command line are : all , plants , archaea, bacteria , eukarya , protists , fungi , metazoa and vertebrates. These will use the NCBI taxonomy as a tree to annotate events in different gene family's histories. | ||
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.. code-block:: bash | ||
$python lshbuilder.py --outpath YourHogProfDirectory --dbtype all --OMA YourOmaDirectory/OmaServer.h5 --nthreads numberOfCPUcores | ||
This should build a taxonomic tree for the genomes contained in the release and then calculate enhanced phylogenies for all HOGs in OMA. | ||
Once the database is completed it can be interogated using a profiler object. Construction and usage of this object should be done using a python script or notebook. | ||
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.. code-block:: python | ||
import HogProf | ||
myproject.do_x() | ||
Troubleshooting | ||
--------------- | ||
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If you encounter any issues while using My Project, please file a bug report on our GitHub repository: https://github.com/user/repo/issues | ||
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Credits | ||
------- | ||
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My Project was created by John Doe. |
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/* Compatability shim for jQuery and underscores.js. | ||
* | ||
* Copyright Sphinx contributors | ||
* Released under the two clause BSD licence | ||
*/ | ||
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/** | ||
* small helper function to urldecode strings | ||
* | ||
* See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL | ||
*/ | ||
jQuery.urldecode = function(x) { | ||
if (!x) { | ||
return x | ||
} | ||
return decodeURIComponent(x.replace(/\+/g, ' ')); | ||
}; | ||
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/** | ||
* small helper function to urlencode strings | ||
*/ | ||
jQuery.urlencode = encodeURIComponent; | ||
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/** | ||
* This function returns the parsed url parameters of the | ||
* current request. Multiple values per key are supported, | ||
* it will always return arrays of strings for the value parts. | ||
*/ | ||
jQuery.getQueryParameters = function(s) { | ||
if (typeof s === 'undefined') | ||
s = document.location.search; | ||
var parts = s.substr(s.indexOf('?') + 1).split('&'); | ||
var result = {}; | ||
for (var i = 0; i < parts.length; i++) { | ||
var tmp = parts[i].split('=', 2); | ||
var key = jQuery.urldecode(tmp[0]); | ||
var value = jQuery.urldecode(tmp[1]); | ||
if (key in result) | ||
result[key].push(value); | ||
else | ||
result[key] = [value]; | ||
} | ||
return result; | ||
}; | ||
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/** | ||
* highlight a given string on a jquery object by wrapping it in | ||
* span elements with the given class name. | ||
*/ | ||
jQuery.fn.highlightText = function(text, className) { | ||
function highlight(node, addItems) { | ||
if (node.nodeType === 3) { | ||
var val = node.nodeValue; | ||
var pos = val.toLowerCase().indexOf(text); | ||
if (pos >= 0 && | ||
!jQuery(node.parentNode).hasClass(className) && | ||
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var span; | ||
var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); | ||
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span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); | ||
} else { | ||
span = document.createElement("span"); | ||
span.className = className; | ||
} | ||
span.appendChild(document.createTextNode(val.substr(pos, text.length))); | ||
node.parentNode.insertBefore(span, node.parentNode.insertBefore( | ||
document.createTextNode(val.substr(pos + text.length)), | ||
node.nextSibling)); | ||
node.nodeValue = val.substr(0, pos); | ||
if (isInSVG) { | ||
var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); | ||
var bbox = node.parentElement.getBBox(); | ||
rect.x.baseVal.value = bbox.x; | ||
rect.y.baseVal.value = bbox.y; | ||
rect.width.baseVal.value = bbox.width; | ||
rect.height.baseVal.value = bbox.height; | ||
rect.setAttribute('class', className); | ||
addItems.push({ | ||
"parent": node.parentNode, | ||
"target": rect}); | ||
} | ||
} | ||
} | ||
else if (!jQuery(node).is("button, select, textarea")) { | ||
jQuery.each(node.childNodes, function() { | ||
highlight(this, addItems); | ||
}); | ||
} | ||
} | ||
var addItems = []; | ||
var result = this.each(function() { | ||
highlight(this, addItems); | ||
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for (var i = 0; i < addItems.length; ++i) { | ||
jQuery(addItems[i].parent).before(addItems[i].target); | ||
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return result; | ||
}; | ||
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/* | ||
* backward compatibility for jQuery.browser | ||
* This will be supported until firefox bug is fixed. | ||
*/ | ||
if (!jQuery.browser) { | ||
jQuery.uaMatch = function(ua) { | ||
ua = ua.toLowerCase(); | ||
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var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || | ||
/(webkit)[ \/]([\w.]+)/.exec(ua) || | ||
/(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || | ||
/(msie) ([\w.]+)/.exec(ua) || | ||
ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || | ||
[]; | ||
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return { | ||
browser: match[ 1 ] || "", | ||
version: match[ 2 ] || "0" | ||
}; | ||
}; | ||
jQuery.browser = {}; | ||
jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; | ||
} |
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