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Commit b14838e3 by Mustafa Tekpinar
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Updated the documentation.

parent 8d766d4d
Showing with 599 additions and 323 deletions
docs/_build/html/.buildinfo
# 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: 1d56d17901c6f429146d20c07a73dc21
config: 22c71542c2e9339759d7f2af8f251cf8
tags: 645f666f9bcd5a90fca523b33c5a78b7
docs/_build/html/_sources/docker.rst.txt
......@@ -29,13 +29,13 @@ file in fasta format:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta
If you don’t have wget, you can try the same command with curl:
.. code:: bash
curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta >aliBLAT.fasta
Please verify that the aliBLAT.fasta file is in the folder.
......@@ -43,7 +43,7 @@ Now, we will download the PDB (Protein Databank) file for BLAT:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/blat-af2.pdb
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/blat-af2.pdb
Single point mutation calculations
----------------------------------
......@@ -81,7 +81,7 @@ In this step, we will use only evolutionary information from an MSA file:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta
After a few minutes of calculation, you must see at least two files named
BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
......@@ -93,7 +93,7 @@ evolutionary information:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
--normweightmode sstjetormax
......@@ -113,13 +113,13 @@ structural information. First, let's do it without structural information:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
-m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
--normweightmode sstjetormax \
-m Stiffler_2015_BLAT_ECOLX.mut
......
docs/_build/html/_sources/installation.rst.txt
......@@ -22,20 +22,115 @@ ESGEMME has the following external dependencies:
These tools should be installed to be able to use ESGEMME.
Getting the source code and preparing the environment:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Preparation of the environment and installation of ESGEMME
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Download the ESGEMME source code from
http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME. Define and export the
environment variable ESGEMME_PATH=/path-to-ESGEMME-directory/
Step by step installation on Ubuntu 22.04
Prepare your environment and install the required packages:
.. code:: bash
sudo apt-get update --fix-missing && \
sudo apt-get install -y --no-install-recommends apt-utils && \
sudo apt-get install -y software-properties-common && \
sudo apt-get install -y autotools-dev && \
sudo apt-get install -y automake && \
sudo apt-get install -y build-essential && \
sudo apt-get install -y python3-dev && \
sudo apt-get install -y python3-pip && \
sudo apt-get install -y r-base r-base-core && \
sudo apt-get install -y muscle && \
sudo apt-get install -y default-jre && \
sudo apt-get install -y ncbi-blast+ && \
sudo apt-get install -y nano && \
sudo apt-get install -y less && \
sudo apt-get install -y wget && \
sudo apt-get install csh && \
sudo apt-get install -y hmmer && \
sudo apt-get install -y libboost-all-dev && \
sudo apt-get clean && \
sudo rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
#Dssp installation
If you are using Ubuntu 20.04, you can install dssp by the following command
.. code:: bash
sudo apt-get install dssp
Otherwise, you can install it from the source by the following commands.
Please note that default dssp in Ubuntu 22.04 is not working properly.
.. code:: bash
wget https://github.com/cmbi/dssp/archive/refs/heads/master.zip && \
unzip -o master.zip && cd dssp-master/ && \
./autogen.sh && \
./configure && \
make && \
sudo make install && \
sudo ln -s /usr/local/bin/mkdssp /usr/local/bin/dssp && \
cd ../ && \
sudo rm -rf dssp-master/ && \
sudo rm -f master.zip
#HHSUITE installation
.. code:: bash
wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz && \
mkdir hhsuite && \
mv hhsuite-3.3.0-AVX2-Linux.tar.gz hhsuite/ && \
cd hhsuite && \
tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz && \
rm -f hhsuite-3.3.0-AVX2-Linux.tar.gz
#Add it to your path permanently inside .bashrc or .profile or .bash_profile
Check the location of hhsuite folder and add it to your path
In my case it was in /home/tekpinar/research/lcqb folder. Therefore, I added the following line
to my .profile file.
PATH="/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:$PATH"
Then
source ~/.profile
#
cd ESGEMME
#Download ESGEMME from http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME repository and go inside the ESGEMME folder.!
.. code:: bash
export ESGEMME_PATH=/path-to-ESGEMME-directory/
cd ESGEMME
Configuring default.conf file
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Inside ESGEMME folder, there is an important file called default.conf.
Inside ESGEMME/esgemme folder, there is an important file called default.conf.
This file contains essential parameters of ESGEMME, such as paths of
external parts, default internal parameters. etc. You have to correct the Software section of this
file according to your system.
.. code:: bash
pip3 install -e . &&\
cd ../
#Installing the required R packages
.. code:: bash
sudo Rscript -e 'install.packages("seqinr", repos="http://cran.us.r-project.org", dependencies=TRUE)'
#Installing secondary programs such as ev_couplings to obtain MSA files.
.. code:: bash
wget https://github.com/debbiemarkslab/plmc/archive/refs/heads/master.zip && \
unzip -o master.zip && \
cd plmc-master && \
make all-openmp32 && \
sudo cp bin/plmc /usr/local/bin/ && \
cd ../ && \
rm -rf master.zip plmc-master
docs/_build/html/_static/_sphinx_javascript_frameworks_compat.js
/* Compatability shim for jQuery and underscores.js.
/*
* _sphinx_javascript_frameworks_compat.js
* ~~~~~~~~~~
*
* Compatability shim for jQuery and underscores.js.
*
* WILL BE REMOVED IN Sphinx 6.0
* xref RemovedInSphinx60Warning
*
* Copyright Sphinx contributors
* Released under the two clause BSD licence
*/
/**
* select a different prefix for underscore
*/
$u = _.noConflict();
/**
* 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
......
docs/_build/html/_static/basic.css
......@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
* :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
* :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
......@@ -324,17 +324,17 @@ aside.sidebar {
p.sidebar-title {
font-weight: bold;
}
nav.contents,
aside.topic,
div.admonition, div.topic, blockquote {
clear: left;
}
/* -- topics ---------------------------------------------------------------- */
nav.contents,
aside.topic,
div.topic {
border: 1px solid #ccc;
padding: 7px;
......@@ -375,6 +375,7 @@ div.sidebar > :last-child,
aside.sidebar > :last-child,
nav.contents > :last-child,
aside.topic > :last-child,
div.topic > :last-child,
div.admonition > :last-child {
margin-bottom: 0;
......@@ -384,6 +385,7 @@ div.sidebar::after,
aside.sidebar::after,
nav.contents::after,
aside.topic::after,
div.topic::after,
div.admonition::after,
blockquote::after {
......@@ -609,6 +611,25 @@ ul.simple p {
margin-bottom: 0;
}
/* Docutils 0.17 and older (footnotes & citations) */
dl.footnote > dt,
dl.citation > dt {
float: left;
margin-right: 0.5em;
}
dl.footnote > dd,
dl.citation > dd {
margin-bottom: 0em;
}
dl.footnote > dd:after,
dl.citation > dd:after {
content: "";
clear: both;
}
/* Docutils 0.18+ (footnotes & citations) */
aside.footnote > span,
div.citation > span {
float: left;
......@@ -633,6 +654,8 @@ div.citation > p:last-of-type:after {
clear: both;
}
/* Footnotes & citations ends */
dl.field-list {
display: grid;
grid-template-columns: fit-content(30%) auto;
......@@ -645,6 +668,10 @@ dl.field-list > dt {
padding-right: 5px;
}
dl.field-list > dt:after {
content: ":";
}
dl.field-list > dd {
padding-left: 0.5em;
margin-top: 0em;
......
docs/_build/html/_static/css/theme.css
This source diff could not be displayed because it is too large. You can view the blob instead.
docs/_build/html/_static/doctools.js
......@@ -4,19 +4,12 @@
*
* Base JavaScript utilities for all Sphinx HTML documentation.
*
* :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
* :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
"use strict";
const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([
"TEXTAREA",
"INPUT",
"SELECT",
"BUTTON",
]);
const _ready = (callback) => {
if (document.readyState !== "loading") {
callback();
......@@ -26,10 +19,72 @@ const _ready = (callback) => {
};
/**
* highlight a given string on a node by wrapping it in
* span elements with the given class name.
*/
const _highlight = (node, addItems, text, className) => {
if (node.nodeType === Node.TEXT_NODE) {
const val = node.nodeValue;
const parent = node.parentNode;
const pos = val.toLowerCase().indexOf(text);
if (
pos >= 0 &&
!parent.classList.contains(className) &&
!parent.classList.contains("nohighlight")
) {
let span;
const closestNode = parent.closest("body, svg, foreignObject");
const isInSVG = closestNode && closestNode.matches("svg");
if (isInSVG) {
span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
} else {
span = document.createElement("span");
span.classList.add(className);
}
span.appendChild(document.createTextNode(val.substr(pos, text.length)));
parent.insertBefore(
span,
parent.insertBefore(
document.createTextNode(val.substr(pos + text.length)),
node.nextSibling
)
);
node.nodeValue = val.substr(0, pos);
if (isInSVG) {
const rect = document.createElementNS(
"http://www.w3.org/2000/svg",
"rect"
);
const bbox = parent.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: parent, target: rect });
}
}
} else if (node.matches && !node.matches("button, select, textarea")) {
node.childNodes.forEach((el) => _highlight(el, addItems, text, className));
}
};
const _highlightText = (thisNode, text, className) => {
let addItems = [];
_highlight(thisNode, addItems, text, className);
addItems.forEach((obj) =>
obj.parent.insertAdjacentElement("beforebegin", obj.target)
);
};
/**
* Small JavaScript module for the documentation.
*/
const Documentation = {
init: () => {
Documentation.highlightSearchWords();
Documentation.initDomainIndexTable();
Documentation.initOnKeyListeners();
},
......@@ -72,6 +127,51 @@ const Documentation = {
},
/**
* highlight the search words provided in the url in the text
*/
highlightSearchWords: () => {
const highlight =
new URLSearchParams(window.location.search).get("highlight") || "";
const terms = highlight.toLowerCase().split(/\s+/).filter(x => x);
if (terms.length === 0) return; // nothing to do
// There should never be more than one element matching "div.body"
const divBody = document.querySelectorAll("div.body");
const body = divBody.length ? divBody[0] : document.querySelector("body");
window.setTimeout(() => {
terms.forEach((term) => _highlightText(body, term, "highlighted"));
}, 10);
const searchBox = document.getElementById("searchbox");
if (searchBox === null) return;
searchBox.appendChild(
document
.createRange()
.createContextualFragment(
'<p class="highlight-link">' +
'<a href="javascript:Documentation.hideSearchWords()">' +
Documentation.gettext("Hide Search Matches") +
"</a></p>"
)
);
},
/**
* helper function to hide the search marks again
*/
hideSearchWords: () => {
document
.querySelectorAll("#searchbox .highlight-link")
.forEach((el) => el.remove());
document
.querySelectorAll("span.highlighted")
.forEach((el) => el.classList.remove("highlighted"));
const url = new URL(window.location);
url.searchParams.delete("highlight");
window.history.replaceState({}, "", url);
},
/**
* helper function to focus on search bar
*/
focusSearchBar: () => {
......@@ -110,11 +210,15 @@ const Documentation = {
)
return;
const blacklistedElements = new Set([
"TEXTAREA",
"INPUT",
"SELECT",
"BUTTON",
]);
document.addEventListener("keydown", (event) => {
// bail for input elements
if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
// bail with special keys
if (event.altKey || event.ctrlKey || event.metaKey) return;
if (blacklistedElements.has(document.activeElement.tagName)) return; // bail for input elements
if (event.altKey || event.ctrlKey || event.metaKey) return; // bail with special keys
if (!event.shiftKey) {
switch (event.key) {
......@@ -136,6 +240,10 @@ const Documentation = {
event.preventDefault();
}
break;
case "Escape":
if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
Documentation.hideSearchWords();
event.preventDefault();
}
}
......
docs/_build/html/_static/documentation_options.js
......@@ -10,5 +10,5 @@ var DOCUMENTATION_OPTIONS = {
SOURCELINK_SUFFIX: '.txt',
NAVIGATION_WITH_KEYS: false,
SHOW_SEARCH_SUMMARY: true,
ENABLE_SEARCH_SHORTCUTS: true,
ENABLE_SEARCH_SHORTCUTS: false,
};
\ No newline at end of file
docs/_build/html/_static/jquery-3.6.0.js 0 → 100644
This source diff could not be displayed because it is too large. You can view the blob instead.
docs/_build/html/_static/language_data.js
......@@ -5,7 +5,7 @@
* This script contains the language-specific data used by searchtools.js,
* namely the list of stopwords, stemmer, scorer and splitter.
*
* :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
* :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
......
docs/_build/html/_static/searchtools.js
......@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for the full-text search.
*
* :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
* :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
......@@ -57,14 +57,14 @@ const _removeChildren = (element) => {
const _escapeRegExp = (string) =>
string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
const _displayItem = (item, searchTerms) => {
const _displayItem = (item, highlightTerms, searchTerms) => {
const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
const [docName, title, anchor, descr, score, _filename] = item;
const [docName, title, anchor, descr] = item;
let listItem = document.createElement("li");
let requestUrl;
......@@ -82,12 +82,13 @@ const _displayItem = (item, searchTerms) => {
requestUrl = docUrlRoot + docName + docFileSuffix;
linkUrl = docName + docLinkSuffix;
}
const params = new URLSearchParams();
params.set("highlight", [...highlightTerms].join(" "));
let linkEl = listItem.appendChild(document.createElement("a"));
linkEl.href = linkUrl + anchor;
linkEl.dataset.score = score;
linkEl.href = linkUrl + "?" + params.toString() + anchor;
linkEl.innerHTML = title;
if (descr)
listItem.appendChild(document.createElement("span")).innerHTML =
listItem.appendChild(document.createElement("span")).innerText =
" (" + descr + ")";
else if (showSearchSummary)
fetch(requestUrl)
......@@ -95,7 +96,7 @@ const _displayItem = (item, searchTerms) => {
.then((data) => {
if (data)
listItem.appendChild(
Search.makeSearchSummary(data, searchTerms)
Search.makeSearchSummary(data, searchTerms, highlightTerms)
);
});
Search.output.appendChild(listItem);
......@@ -115,14 +116,15 @@ const _finishSearch = (resultCount) => {
const _displayNextItem = (
results,
resultCount,
highlightTerms,
searchTerms
) => {
// results left, load the summary and display it
// this is intended to be dynamic (don't sub resultsCount)
if (results.length) {
_displayItem(results.pop(), searchTerms);
_displayItem(results.pop(), highlightTerms, searchTerms);
setTimeout(
() => _displayNextItem(results, resultCount, searchTerms),
() => _displayNextItem(results, resultCount, highlightTerms, searchTerms),
5
);
}
......@@ -153,8 +155,10 @@ const Search = {
_pulse_status: -1,
htmlToText: (htmlString) => {
const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() });
const htmlElement = document
.createRange()
.createContextualFragment(htmlString);
_removeChildren(htmlElement.querySelectorAll(".headerlink"));
const docContent = htmlElement.querySelector('[role="main"]');
if (docContent !== undefined) return docContent.textContent;
console.warn(
......@@ -235,12 +239,6 @@ const Search = {
* execute search (requires search index to be loaded)
*/
query: (query) => {
const filenames = Search._index.filenames;
const docNames = Search._index.docnames;
const titles = Search._index.titles;
const allTitles = Search._index.alltitles;
const indexEntries = Search._index.indexentries;
// stem the search terms and add them to the correct list
const stemmer = new Stemmer();
const searchTerms = new Set();
......@@ -268,10 +266,6 @@ const Search = {
}
});
if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js
localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" "))
}
// console.debug("SEARCH: searching for:");
// console.info("required: ", [...searchTerms]);
// console.info("excluded: ", [...excludedTerms]);
......@@ -280,40 +274,6 @@ const Search = {
let results = [];
_removeChildren(document.getElementById("search-progress"));
const queryLower = query.toLowerCase();
for (const [title, foundTitles] of Object.entries(allTitles)) {
if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) {
for (const [file, id] of foundTitles) {
let score = Math.round(100 * queryLower.length / title.length)
results.push([
docNames[file],
titles[file] !== title ? `${titles[file]} > ${title}` : title,
id !== null ? "#" + id : "",
null,
score,
filenames[file],
]);
}
}
}
// search for explicit entries in index directives
for (const [entry, foundEntries] of Object.entries(indexEntries)) {
if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) {
for (const [file, id] of foundEntries) {
let score = Math.round(100 * queryLower.length / entry.length)
results.push([
docNames[file],
titles[file],
id ? "#" + id : "",
null,
score,
filenames[file],
]);
}
}
}
// lookup as object
objectTerms.forEach((term) =>
results.push(...Search.performObjectSearch(term, objectTerms))
......@@ -360,7 +320,7 @@ const Search = {
// console.info("search results:", Search.lastresults);
// print the results
_displayNextItem(results, results.length, searchTerms);
_displayNextItem(results, results.length, highlightTerms, searchTerms);
},
/**
......@@ -441,8 +401,8 @@ const Search = {
// prepare search
const terms = Search._index.terms;
const titleTerms = Search._index.titleterms;
const filenames = Search._index.filenames;
const docNames = Search._index.docnames;
const filenames = Search._index.filenames;
const titles = Search._index.titles;
const scoreMap = new Map();
......@@ -539,15 +499,16 @@ const Search = {
/**
* helper function to return a node containing the
* search summary for a given text. keywords is a list
* of stemmed words.
* of stemmed words, highlightWords is the list of normal, unstemmed
* words. the first one is used to find the occurrence, the
* latter for highlighting it.
*/
makeSearchSummary: (htmlText, keywords) => {
const text = Search.htmlToText(htmlText);
makeSearchSummary: (htmlText, keywords, highlightWords) => {
const text = Search.htmlToText(htmlText).toLowerCase();
if (text === "") return null;
const textLower = text.toLowerCase();
const actualStartPosition = [...keywords]
.map((k) => textLower.indexOf(k.toLowerCase()))
.map((k) => text.indexOf(k.toLowerCase()))
.filter((i) => i > -1)
.slice(-1)[0];
const startWithContext = Math.max(actualStartPosition - 120, 0);
......@@ -555,9 +516,13 @@ const Search = {
const top = startWithContext === 0 ? "" : "...";
const tail = startWithContext + 240 < text.length ? "..." : "";
let summary = document.createElement("p");
let summary = document.createElement("div");
summary.classList.add("context");
summary.textContent = top + text.substr(startWithContext, 240).trim() + tail;
summary.innerText = top + text.substr(startWithContext, 240).trim() + tail;
highlightWords.forEach((highlightWord) =>
_highlightText(summary, highlightWord, "highlighted")
);
return summary;
},
......
docs/_build/html/analysis.html
......@@ -11,11 +11,11 @@
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/sphinx_highlight.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
......
docs/_build/html/docker.html
......@@ -11,11 +11,11 @@
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/doctools.js"></script>
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<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
......@@ -57,7 +57,6 @@
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESGEMME Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html#raw-esgemme-scores-and-their-interpretation">Raw ESGEMME Scores and Their Interpretation</a></li>
<li class="toctree-l1"><a class="reference internal" href="input-preparation.html">Preparing Your Own Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
</ul>
......@@ -97,8 +96,8 @@ commands.</p>
<p>Let’s start our favorite terminal app.</p>
<p>You must create a folder called docker-tutorial and go to that empty
folder:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mkdir<span class="w"> </span>docker-tutorial
<span class="nb">cd</span><span class="w"> </span>docker-tutorial
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mkdir docker-tutorial
<span class="nb">cd</span> docker-tutorial
</pre></div>
</div>
</section>
......@@ -107,35 +106,35 @@ folder:</p>
<p>Let’s download the sample data provided in the ESGEMME repository for
this exercise. First, we will download the multiple sequence alignment
file in fasta format:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget<span class="w"> </span>http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta
</pre></div>
</div>
<p>If you don’t have wget, you can try the same command with curl:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>curl<span class="w"> </span>http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta &gt;aliBLAT.fasta
</pre></div>
</div>
<p>Please verify that the aliBLAT.fasta file is in the folder.</p>
<p>Now, we will download the PDB (Protein Databank) file for BLAT:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget<span class="w"> </span>http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/blat-af2.pdb
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/blat-af2.pdb
</pre></div>
</div>
</section>
<section id="single-point-mutation-calculations">
<h2>Single point mutation calculations<a class="headerlink" href="#single-point-mutation-calculations" title="Permalink to this heading"></a></h2>
<p>In order to make sure that the docker is installed:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo<span class="w"> </span>docker<span class="w"> </span>-h
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo docker -h
</pre></div>
</div>
<p>If it shows you a list of options, you are on a good track. On MacOS,
you may not need ‘sudo’ word before the docker command at all.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo<span class="w"> </span>docker<span class="w"> </span>run<span class="w"> </span>-ti<span class="w"> </span>--rm<span class="w"> </span>--mount<span class="w"> </span><span class="nv">type</span><span class="o">=</span>bind,source<span class="o">=</span><span class="nv">$PWD</span>,target<span class="o">=</span>/home/tekpinar/research/myexample<span class="w"> </span><span class="se">\</span>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo docker run -ti --rm --mount <span class="nv">type</span><span class="o">=</span>bind,source<span class="o">=</span><span class="nv">$PWD</span>,target<span class="o">=</span>/home/tekpinar/research/myexample <span class="se">\</span>
tekpinar/esgemme-docker:v1.3.0
</pre></div>
</div>
<p>You are in the container (your virtual operating system) now. You
created a folder called myexample in your container with the previous
command. Let’s change to that folder.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span><span class="w"> </span>../myexample/
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> ../myexample/
</pre></div>
</div>
<p>When you check the data in that folder with ‘ls’ command, you are
......@@ -145,7 +144,7 @@ docker container are pointing to the same place.</p>
<section id="obtaining-the-entire-single-point-mutation-landscape">
<h3>Obtaining the entire single point mutation landscape<a class="headerlink" href="#obtaining-the-entire-single-point-mutation-landscape" title="Permalink to this heading"></a></h3>
<p>In this step, we will use only evolutionary information from an MSA file:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>python<span class="w"> </span><span class="nv">$ESGEMME_PATH</span>/esgemme.py<span class="w"> </span>aliBLAT.fasta<span class="w"> </span>-r<span class="w"> </span>input<span class="w"> </span>-f<span class="w"> </span>aliBLAT.fasta
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>esgemme aliBLAT.fasta -r input -f aliBLAT.fasta
</pre></div>
</div>
<p>After a few minutes of calculation, you must see at least two files named
......@@ -154,9 +153,9 @@ the entire single point mutational landscape of BLAT protein in these
files.</p>
<p>If you want to utilize structural information (highly recommended) as well as
evolutionary information:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>python<span class="w"> </span><span class="nv">$ESGEMME_PATH</span>/esgemme.py<span class="w"> </span>aliBLAT.fasta<span class="w"> </span>-r<span class="w"> </span>input<span class="w"> </span>-f<span class="w"> </span>aliBLAT.fasta<span class="w"> </span><span class="se">\</span>
--pdbfile<span class="w"> </span>blat-af2.pdb<span class="w"> </span><span class="se">\</span>
--normweightmode<span class="w"> </span>sstjetormax
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>esgemme aliBLAT.fasta -r input -f aliBLAT.fasta <span class="se">\</span>
--pdbfile blat-af2.pdb <span class="se">\</span>
--normweightmode sstjetormax
</pre></div>
</div>
</section>
......@@ -166,19 +165,19 @@ evolutionary information:</p>
you have to prepare a mut file. The format is a simple text file and
each line contains a single point mutation such as D26A….
Fortunately, we have an example mut in data folder of ESGEMME repository.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget<span class="w"> </span>http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/master/data/Stiffler_2015_BLAT_ECOLX.mut
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/master/data/Stiffler_2015_BLAT_ECOLX.mut
</pre></div>
</div>
<p>Similar to the previous step, there are two possible ways to do the calculations: with or without
structural information. First, let’s do it without structural information:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>python<span class="w"> </span><span class="nv">$ESGEMME_PATH</span>/esgemme.py<span class="w"> </span>aliBLAT.fasta<span class="w"> </span>-r<span class="w"> </span>input<span class="w"> </span>-f<span class="w"> </span>aliBLAT.fasta<span class="w"> </span><span class="se">\</span>
-m<span class="w"> </span>Stiffler_2015_BLAT_ECOLX.mut
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>esgemme aliBLAT.fasta -r input -f aliBLAT.fasta <span class="se">\</span>
-m Stiffler_2015_BLAT_ECOLX.mut
</pre></div>
</div>
<p>You can include structural information in the following way:
.. code:: bash</p>
<blockquote>
<div><p>python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta –pdbfile blat-af2.pdb –normweightmode sstjetormax -m Stiffler_2015_BLAT_ECOLX.mut</p>
<div><p>esgemme aliBLAT.fasta -r input -f aliBLAT.fasta –pdbfile blat-af2.pdb –normweightmode sstjetormax -m Stiffler_2015_BLAT_ECOLX.mut</p>
</div></blockquote>
<p>You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output
format is completely different from the entire mutational landscape scanning file.
......
docs/_build/html/genindex.html
......@@ -10,11 +10,11 @@
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
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<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/doctools.js"></script>
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<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="#" />
<link rel="search" title="Search" href="search.html" />
......
docs/_build/html/index.html
......@@ -11,11 +11,11 @@
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
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......@@ -98,7 +98,7 @@
</li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="installation.html#installing-the-dependencies">Installing the dependencies:</a></li>
<li class="toctree-l2"><a class="reference internal" href="installation.html#getting-the-source-code-and-preparing-the-environment">Getting the source code and preparing the environment:</a></li>
<li class="toctree-l2"><a class="reference internal" href="installation.html#preparation-of-the-environment-and-installation-of-esgemme">Preparation of the environment and installation of ESGEMME</a></li>
<li class="toctree-l2"><a class="reference internal" href="installation.html#configuring-default-conf-file">Configuring default.conf file</a></li>
</ul>
</li>
......
docs/_build/html/input-preparation.html
......@@ -11,11 +11,11 @@
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/doctools.js"></script>
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<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
......@@ -46,7 +46,6 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESGEMME Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html#raw-esgemme-scores-and-their-interpretation">Raw ESGEMME Scores and Their Interpretation</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Preparing Your Own Input</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#preparing-your-input-msa-and-pdb-with-colabfold">Preparing Your Input MSA and PDB with Colabfold</a></li>
</ul>
......@@ -109,25 +108,25 @@ We have to clean those gaps. We can do that with a GUI program like Ugene
or Jalview. However, it is a labor intensive procedure. Here, I will use a
small tool that I developed and added to the ESGEMME docker image that I created.</p></li>
<li><p>Start the docker image with the following command:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo<span class="w"> </span>docker<span class="w"> </span>run<span class="w"> </span>-ti<span class="w"> </span>--rm<span class="w"> </span>--mount<span class="w"> </span><span class="nv">type</span><span class="o">=</span>bind,source<span class="o">=</span><span class="nv">$PWD</span>,target<span class="o">=</span>/home/tekpinar/research/myexample<span class="w"> </span><span class="se">\</span>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo docker run -ti --rm --mount <span class="nv">type</span><span class="o">=</span>bind,source<span class="o">=</span><span class="nv">$PWD</span>,target<span class="o">=</span>/home/tekpinar/research/myexample <span class="se">\</span>
tekpinar/esgemme-docker:v1.3.0
</pre></div>
</div>
</li>
<li><p>Now, change the directory to myexample folder.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span><span class="w"> </span>../myexample/
ls<span class="w"> </span>-l
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> ../myexample/
ls -l
</pre></div>
</div>
<p>We are supposed to see our a3m and pdb files in this folder.</p>
</li>
<li><p>Let’s use a small script from hhsuite to convert a3m file to fasta format.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>reformat.pl<span class="w"> </span>a3m<span class="w"> </span>fas<span class="w"> </span>AKE.a3m<span class="w"> </span>AKE.fasta
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>reformat.pl a3m fas AKE.a3m AKE.fasta
</pre></div>
</div>
</li>
<li><p>Final step and we are there:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>demust<span class="w"> </span>removegaps<span class="w"> </span>-i<span class="w"> </span>AKE.fasta<span class="w"> </span>-o<span class="w"> </span>AKE_nogaps.fasta
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>demust removegaps -i AKE.fasta -o AKE_nogaps.fasta
</pre></div>
</div>
</li>
......
docs/_build/html/installation.html
......@@ -11,11 +11,11 @@
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/sphinx_highlight.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
......@@ -45,11 +45,10 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESGEMME Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html#raw-esgemme-scores-and-their-interpretation">Raw ESGEMME Scores and Their Interpretation</a></li>
<li class="toctree-l1"><a class="reference internal" href="input-preparation.html">Preparing Your Own Input</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#installing-the-dependencies">Installing the dependencies:</a></li>
<li class="toctree-l2"><a class="reference internal" href="#getting-the-source-code-and-preparing-the-environment">Getting the source code and preparing the environment:</a></li>
<li class="toctree-l2"><a class="reference internal" href="#preparation-of-the-environment-and-installation-of-esgemme">Preparation of the environment and installation of ESGEMME</a></li>
<li class="toctree-l2"><a class="reference internal" href="#configuring-default-conf-file">Configuring default.conf file</a></li>
</ul>
</li>
......@@ -101,21 +100,91 @@ steps required to install it from the source.</p>
</ul>
<p>These tools should be installed to be able to use ESGEMME.</p>
</section>
<section id="getting-the-source-code-and-preparing-the-environment">
<h2>Getting the source code and preparing the environment:<a class="headerlink" href="#getting-the-source-code-and-preparing-the-environment" title="Permalink to this heading"></a></h2>
<p>Download the ESGEMME source code from
<a class="reference external" href="http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME">http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME</a>. Define and export the
environment variable ESGEMME_PATH=/path-to-ESGEMME-directory/</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">ESGEMME_PATH</span><span class="o">=</span>/path-to-ESGEMME-directory/
<section id="preparation-of-the-environment-and-installation-of-esgemme">
<h2>Preparation of the environment and installation of ESGEMME<a class="headerlink" href="#preparation-of-the-environment-and-installation-of-esgemme" title="Permalink to this heading"></a></h2>
<p>Step by step installation on Ubuntu 22.04</p>
<p>Prepare your environment and install the required packages:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo apt-get update --fix-missing <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y --no-install-recommends apt-utils <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y software-properties-common <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y autotools-dev <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y automake <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y build-essential <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y python3-dev <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y python3-pip <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y r-base r-base-core <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y muscle <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y default-jre <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y ncbi-blast+ <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y nano <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y less <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y wget <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install csh <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y hmmer <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get install -y libboost-all-dev <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo apt-get clean <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
</pre></div>
</div>
<p>#Dssp installation
If you are using Ubuntu 20.04, you can install dssp by the following command
.. code:: bash</p>
<blockquote>
<div><p>sudo apt-get install dssp</p>
</div></blockquote>
<p>Otherwise, you can install it from the source by the following commands.
Please note that default dssp in Ubuntu 22.04 is not working properly.
.. code:: bash</p>
<blockquote>
<div><p>wget <a class="reference external" href="https://github.com/cmbi/dssp/archive/refs/heads/master.zip">https://github.com/cmbi/dssp/archive/refs/heads/master.zip</a> &amp;&amp; unzip -o master.zip &amp;&amp; cd dssp-master/ &amp;&amp; ./autogen.sh &amp;&amp; ./configure &amp;&amp; make &amp;&amp; sudo make install &amp;&amp; sudo ln -s /usr/local/bin/mkdssp /usr/local/bin/dssp &amp;&amp; cd ../ &amp;&amp; sudo rm -rf dssp-master/ &amp;&amp; sudo rm -f master.zip</p>
</div></blockquote>
<p>#HHSUITE installation
.. code:: bash</p>
<blockquote>
<div><p>wget <a class="reference external" href="https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz">https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz</a> &amp;&amp; mkdir hhsuite &amp;&amp; mv hhsuite-3.3.0-AVX2-Linux.tar.gz hhsuite/ &amp;&amp; cd hhsuite &amp;&amp; tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz &amp;&amp; rm -f hhsuite-3.3.0-AVX2-Linux.tar.gz</p>
</div></blockquote>
<p>#Add it to your path permanently inside .bashrc or .profile or .bash_profile
Check the location of hhsuite folder and add it to your path
In my case it was in /home/tekpinar/research/lcqb folder. Therefore, I added the following line
to my .profile file.
PATH=”/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:$PATH”</p>
<p>Then
source ~/.profile</p>
<p>#</p>
<blockquote>
<div><p>cd ESGEMME</p>
</div></blockquote>
<p>#Download ESGEMME from <a class="reference external" href="http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME">http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME</a> repository and go inside the ESGEMME folder.!
.. code:: bash</p>
<blockquote>
<div><p>cd ESGEMME</p>
</div></blockquote>
</section>
<section id="configuring-default-conf-file">
<h2>Configuring default.conf file<a class="headerlink" href="#configuring-default-conf-file" title="Permalink to this heading"></a></h2>
<p>Inside ESGEMME folder, there is an important file called default.conf.
<p>Inside ESGEMME/esgemme folder, there is an important file called default.conf.
This file contains essential parameters of ESGEMME, such as paths of
external parts, default internal parameters. etc. You have to correct the Software section of this
file according to your system.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip3 install -e . <span class="o">&amp;&amp;</span><span class="se">\</span>
<span class="nb">cd</span> ../
</pre></div>
</div>
<p>#Installing the required R packages
.. code:: bash</p>
<blockquote>
<div><p>sudo Rscript -e ‘install.packages(“seqinr”, repos=”<a class="reference external" href="http://cran.us.r-project.org">http://cran.us.r-project.org</a>”, dependencies=TRUE)’</p>
</div></blockquote>
<p>#Installing secondary programs such as ev_couplings to obtain MSA files.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget https://github.com/debbiemarkslab/plmc/archive/refs/heads/master.zip <span class="o">&amp;&amp;</span> <span class="se">\</span>
unzip -o master.zip <span class="o">&amp;&amp;</span> <span class="se">\</span>
<span class="nb">cd</span> plmc-master <span class="o">&amp;&amp;</span> <span class="se">\</span>
make all-openmp32 <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo cp bin/plmc /usr/local/bin/ <span class="o">&amp;&amp;</span> <span class="se">\</span>
<span class="nb">cd</span> ../ <span class="o">&amp;&amp;</span> <span class="se">\</span>
rm -rf master.zip plmc-master
</pre></div>
</div>
</section>
</section>
......
docs/_build/html/search.html
......@@ -11,11 +11,11 @@
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......@@ -18,7 +14,7 @@
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......@@ -63,11 +64,12 @@
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docs/_build/latex/esgemme.toc
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\contentsline {section}{\numberline {1.2}Getting the example input data}{1}{section.1.2}%
......@@ -15,6 +15,6 @@
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......@@ -103,27 +103,4 @@
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% Sphinx redefinitions
% Originally to obtain a straight single quote via package textcomp, then
% to fix problems for the 5.0.0 inline code highlighting (captions!).
% The \text is from amstext, a dependency of sphinx.sty. It is here only
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docs/_build/latex/sphinxlatexobjects.sty
......@@ -119,7 +119,7 @@
\pysig@restore@itemsep@and@parskip
}
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\newlength{\py@argswidth}
\newcommand{\py@sigparams}[2]{%
......
docs/_build/latex/sphinxlatexshadowbox.sty
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% Provides support for this output mark-up from Sphinx latex writer:
%
......@@ -16,58 +16,48 @@
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%
% Docutils does not allow topic to be nested within topics or other body
% elements. But the LaTeX code here does allow it:
%
% - a topic inside another topic would be rendered in a minipage (thus not
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%
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{%
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% mode; but in context of framed.sty's \FrameCommand TeX is already
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\def\FrameCommand {\spx@boxes@fcolorbox}%
% 6.2.0 adds support for div.topic_box-decoration-break=slice.
% (it is yet undecided if slice style should inhibit a bottom shadow)
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\def\FirstFrameCommand
{\spx@boxes@fcolorbox@setup@openbottom\FrameCommand}%
\def\MidFrameCommand
{\spx@boxes@fcolorbox@setup@openboth \FrameCommand}%
\def\LastFrameCommand
{\spx@boxes@fcolorbox@setup@opentop \FrameCommand}%
\fi
{\def\FrameCommand {\spx@ShadowFBox }%
\advance\spx@image@maxheight
-\dimexpr\spx@boxes@border@top+\spx@boxes@border@bottom
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% configure framed.sty not to add extra vertical spacing
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......@@ -83,7 +73,7 @@
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% adjust \hsize to what the contents must use
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% adjust LaTeX parameters to behave properly in indented/quoted contexts
......@@ -96,15 +86,9 @@
\@minipagerestore
\@setminipage
}%
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{% insert the "endminipage" code
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......
docs/_build/latex/sphinxlatexstyleheadings.sty
%% TITLES
%
% change this info string if making any custom modification
\ProvidesFile{sphinxlatexstyleheadings.sty}[2023/02/11 headings]
\ProvidesFile{sphinxlatexstyleheadings.sty}[2021/01/27 headings]
\RequirePackage[nobottomtitles*]{titlesec}
\@ifpackagelater{titlesec}{2016/03/15}%
......@@ -25,7 +25,6 @@
******** and Sphinx could not patch it, perhaps because your local ...|^^J%
******** copy is already fixed without a changed release date. .......|^^J%
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}%
}{}
......@@ -36,15 +35,13 @@
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{\py@TitleColor\thesubsection}{0.5em}{\py@TitleColor}
% \normalsize added as work-around to a lualatex-ja upstream problem
% https://osdn.net/projects/luatex-ja/ticket/47321
\titleformat{\subsubsection}{\normalsize\py@HeaderFamily}%
\titleformat{\subsubsection}{\py@HeaderFamily}%
{\py@TitleColor\thesubsubsection}{0.5em}{\py@TitleColor}
% By default paragraphs (and subsubsections) will not be numbered because
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\titleformat{\paragraph}{\normalsize\py@HeaderFamily}%
\titleformat{\paragraph}{\py@HeaderFamily}%
{\py@TitleColor\theparagraph}{0.5em}{\py@TitleColor}
\titleformat{\subparagraph}{\normalsize\py@HeaderFamily}%
\titleformat{\subparagraph}{\py@HeaderFamily}%
{\py@TitleColor\thesubparagraph}{0.5em}{\py@TitleColor}
......
docs/_build/latex/sphinxlatexstyletext.sty
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%
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\ProvidesFile{sphinxlatexstyletext.sty}[2023/03/26 text styling]
\ProvidesFile{sphinxlatexstyletext.sty}[2021/12/06 text styling]
% Basically everything here consists of macros which are part of the latex
% markup produced by the Sphinx latex writer
% But those arise rather from the default definitions of the respective
% latex environments done in sphinxlatexadmonitions.sty
\def\sphinxstylenotetitle #1{\sphinxstrong{#1} }
\let\sphinxstylehinttitle \sphinxstylenotetitle % #1 holds the localized notice name
\let\sphinxstyleimportanttitle\sphinxstylenotetitle % followed by a colon
\let\sphinxstyletiptitle \sphinxstylenotetitle
\let\sphinxstylewarningtitle \sphinxstylenotetitle
\let\sphinxstylecautiontitle \sphinxstylenotetitle
\let\sphinxstyleattentiontitle\sphinxstylenotetitle
\let\sphinxstyledangertitle \sphinxstylenotetitle
\let\sphinxstyleerrortitle \sphinxstylenotetitle
\def\sphinxstyleseealsotitle#1{\sphinxstrong{#1}\par\nopagebreak}
%
% A utility to remove a final colon. Removing last token is not easy in
% LaTeX, and there are additional complications:
% - some languages will make the : "active" in document body,
% - the generic admonition ends up using "note", so for \sphinxnotetitle to
% use it safely, the utility has to allow an input not having any final colon.
% - a bit far-fetched but maybe there is more than one colon inside the input
% (possible from a generic admonition title).
% Hence the scary code.
\def\sphinxremovefinalcolon#1{% #1 is the "active" : TeX token
\protected\def\sphinxremovefinalcolon ##1{%
% complications due to : possibly "active"
\begingroup\ifnum\catcode`:=\active
\def\x####1#1\relax{####1}%
\else\def\x####1:\relax{####1}\fi
\expandafter\endgroup\x##1\relax
% trick to let \x work also if input ##1 has no ending colon
\@gobblefour#1\relax:\relax\relax\relax
}%
}% end of wrapper to inject active :
\begingroup\catcode`:\active\expandafter\endgroup\sphinxremovefinalcolon:
% See doc/latex.rst for an example.
% Some custom font markup commands.
\protected\def\sphinxstrong#1{\textbf{#1}}
\protected\def\sphinxcode#1{\texttt{#1}}
......@@ -54,8 +19,6 @@
\protected\def\sphinxaccelerator#1{\underline{#1}}
\protected\def\sphinxcrossref#1{\emph{#1}}
\protected\def\sphinxtermref#1{\emph{#1}}
\protected\def\sphinxsamedocref#1{\emph{#1}}
\protected\def\sphinxparam#1{\emph{#1}}
% \optional is used for ``[, arg]``, i.e. desc_optional nodes.
\long\protected\def\sphinxoptional#1{%
{\textnormal{\Large[}}{#1}\hspace{0.5mm}{\textnormal{\Large]}}}
......@@ -76,7 +39,6 @@
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\protected\def\sphinxstylesidebarsubtitle #1{~\\\textbf{#1} \smallskip}
% \text.. commands do not allow multiple paragraphs
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\protected\def\sphinxstyleemphasis #1{\emph{#1}}
\protected\def\sphinxstyleliteralemphasis#1{\emph{\sphinxcode{#1}}}
......@@ -84,8 +46,8 @@
\protected\def\sphinxstyleliteralstrong#1{\sphinxbfcode{#1}}
\protected\def\sphinxstyleabbreviation #1{\textsc{#1}}
\protected\def\sphinxstyleliteralintitle#1{\sphinxcode{#1}}
\newcommand*\sphinxstylecodecontinued[1]{{\footnotesize(#1)}}%
\newcommand*\sphinxstylecodecontinues[1]{{\footnotesize(#1)}}%
\newcommand*\sphinxstylecodecontinued[1]{\footnotesize(#1)}%
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% figure legend comes after caption and may contain arbitrary body elements
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% reduce hyperref "Token not allowed in a PDF string" warnings on PDF builds
......@@ -105,9 +67,7 @@
\let\sphinxemail \@firstofone
\let\sphinxcrossref \@firstofone
\let\sphinxtermref \@firstofone
\let\sphinxsamedocref\@firstofone
\let\sphinxhyphen\sphinxhyphenforbookmarks
\def\PYG#1#2{#2}% (can not yet appear in section titles, but perhaps in future)
}}
% Special characters
......
docs/_build/latex/sphinxpackagefootnote.sty
\NeedsTeXFormat{LaTeX2e}
\ProvidesPackage{sphinxpackagefootnote}%
[2022/08/15 v5.3.0 Sphinx custom footnotehyper package (Sphinx team)]
[2022/02/12 v4.5.0 Sphinx custom footnotehyper package (Sphinx team)]
%%
%% Package: sphinxpackagefootnote
%% Version: based on footnotehyper.sty 2021/02/04 v1.1d
......@@ -338,7 +338,6 @@
}%
% slight reformulation for Sphinx
\def\FNH@bad@makefntext@alert{%
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\PackageWarningNoLine{sphinxpackagefootnote}%
{Footnotes will be sub-optimal, sorry. This is due to the document class or^^J
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......
docs/docker.rst
......@@ -29,13 +29,13 @@ file in fasta format:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta
If you don’t have wget, you can try the same command with curl:
.. code:: bash
curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta >aliBLAT.fasta
Please verify that the aliBLAT.fasta file is in the folder.
......@@ -43,7 +43,7 @@ Now, we will download the PDB (Protein Databank) file for BLAT:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/blat-af2.pdb
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/blat-af2.pdb
Single point mutation calculations
----------------------------------
......@@ -81,7 +81,7 @@ In this step, we will use only evolutionary information from an MSA file:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta
After a few minutes of calculation, you must see at least two files named
BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
......@@ -93,7 +93,7 @@ evolutionary information:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
--normweightmode sstjetormax
......@@ -113,13 +113,13 @@ structural information. First, let's do it without structural information:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
-m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
--normweightmode sstjetormax \
-m Stiffler_2015_BLAT_ECOLX.mut
......
docs/installation.rst
......@@ -22,20 +22,115 @@ ESGEMME has the following external dependencies:
These tools should be installed to be able to use ESGEMME.
Getting the source code and preparing the environment:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Preparation of the environment and installation of ESGEMME
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Download the ESGEMME source code from
http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME. Define and export the
environment variable ESGEMME_PATH=/path-to-ESGEMME-directory/
Step by step installation on Ubuntu 22.04
Prepare your environment and install the required packages:
.. code:: bash
sudo apt-get update --fix-missing && \
sudo apt-get install -y --no-install-recommends apt-utils && \
sudo apt-get install -y software-properties-common && \
sudo apt-get install -y autotools-dev && \
sudo apt-get install -y automake && \
sudo apt-get install -y build-essential && \
sudo apt-get install -y python3-dev && \
sudo apt-get install -y python3-pip && \
sudo apt-get install -y r-base r-base-core && \
sudo apt-get install -y muscle && \
sudo apt-get install -y default-jre && \
sudo apt-get install -y ncbi-blast+ && \
sudo apt-get install -y nano && \
sudo apt-get install -y less && \
sudo apt-get install -y wget && \
sudo apt-get install csh && \
sudo apt-get install -y hmmer && \
sudo apt-get install -y libboost-all-dev && \
sudo apt-get clean && \
sudo rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
#Dssp installation
If you are using Ubuntu 20.04, you can install dssp by the following command
.. code:: bash
sudo apt-get install dssp
Otherwise, you can install it from the source by the following commands.
Please note that default dssp in Ubuntu 22.04 is not working properly.
.. code:: bash
wget https://github.com/cmbi/dssp/archive/refs/heads/master.zip && \
unzip -o master.zip && cd dssp-master/ && \
./autogen.sh && \
./configure && \
make && \
sudo make install && \
sudo ln -s /usr/local/bin/mkdssp /usr/local/bin/dssp && \
cd ../ && \
sudo rm -rf dssp-master/ && \
sudo rm -f master.zip
#HHSUITE installation
.. code:: bash
wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz && \
mkdir hhsuite && \
mv hhsuite-3.3.0-AVX2-Linux.tar.gz hhsuite/ && \
cd hhsuite && \
tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz && \
rm -f hhsuite-3.3.0-AVX2-Linux.tar.gz
#Add it to your path permanently inside .bashrc or .profile or .bash_profile
Check the location of hhsuite folder and add it to your path
In my case it was in /home/tekpinar/research/lcqb folder. Therefore, I added the following line
to my .profile file.
PATH="/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:$PATH"
Then
source ~/.profile
#
cd ESGEMME
#Download ESGEMME from http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME repository and go inside the ESGEMME folder.!
.. code:: bash
export ESGEMME_PATH=/path-to-ESGEMME-directory/
cd ESGEMME
Configuring default.conf file
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Inside ESGEMME folder, there is an important file called default.conf.
Inside ESGEMME/esgemme folder, there is an important file called default.conf.
This file contains essential parameters of ESGEMME, such as paths of
external parts, default internal parameters. etc. You have to correct the Software section of this
file according to your system.
.. code:: bash
pip3 install -e . &&\
cd ../
#Installing the required R packages
.. code:: bash
sudo Rscript -e 'install.packages("seqinr", repos="http://cran.us.r-project.org", dependencies=TRUE)'
#Installing secondary programs such as ev_couplings to obtain MSA files.
.. code:: bash
wget https://github.com/debbiemarkslab/plmc/archive/refs/heads/master.zip && \
unzip -o master.zip && \
cd plmc-master && \
make all-openmp32 && \
sudo cp bin/plmc /usr/local/bin/ && \
cd ../ && \
rm -rf master.zip plmc-master
esgemme/computePred.R
......@@ -86,20 +86,12 @@ if ((normWeightMode=="max")){
}
}else if (normWeightMode=="tjetormax"){
print("Using tjetormax")
print("Using tjetormax with inverse CV")
for (row in 1:nrow(jet)) {
if(sum(colnames(jet)=="traceMax")==1){
if((jet[row, "traceMax"]>jet[row, "pc"]) & (jet[row, "traceMax"]>jet[row, "cv"])){
trace<-append(trace, jet[row, "traceMax"])
}else{
trace<-append(trace, max((jet[row, "traceMax"]+jet[row, "pc"])/2.0, max((jet[row, "traceMax"]+jet[row, "cv"])/2.0, (jet[row, "pc"]+jet[row, "cv"])/2.0 )))
}
trace<-append(trace, max((jet[row, "traceMax"]+jet[row, "pc"])/2.0, max((jet[row, "traceMax"]+1.0-jet[row, "cv"])/2.0, (jet[row, "pc"]+1.0-jet[row, "cv"])/2.0 )))
}else{
if((jet[row, "trace"]>jet[row, "pc"]) & (jet[row, "trace"]>jet[row, "cv"])){
trace<-append(trace, jet[row, "trace"])
}else{
trace<-append(trace, max((jet[row, "trace"]+jet[row, "pc"])/2.0, max((jet[row, "trace"]+jet[row, "cv"])/2.0, (jet[row, "pc"]+jet[row, "cv"])/2.0 )))
}
trace<-append(trace, max((jet[row, "trace"]+jet[row, "pc"])/2.0, max((jet[row, "trace"]+1.0-jet[row, "cv"])/2.0, (jet[row, "pc"]+1.0-jet[row, "cv"])/2.0 )))
}
}
}else{
......
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