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PRESCOTT
Commit 1fd6d4c4 by Mustafa Tekpinar
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Updated documentation.

parent 19352aaf
Showing with 163 additions and 160 deletions
Dockerfile
......@@ -112,5 +112,5 @@ RUN pip3 install https://github.com/debbiemarkslab/EVcouplings/archive/develop.z
#If you want to use the docker image like an executable file:
# Please note that you must have aliBLAT.fasta and blat-af2.pdb inside your current folder and run this command!
# sudo docker run --rm -v $PWD:/home/tekpinar/research/lcqb tekpinar/prescott-docker:v1.4.0 escott aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-af2.pdb
# sudo docker run --rm -v $PWD:/home/tekpinar/research/lcqb tekpinar/prescott-docker:v1.4.0 escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
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: fe2e7449c75c4a1331acfe403ef4e427
config: dbe0b599dc686a00746813e2a7a94d25
tags: 645f666f9bcd5a90fca523b33c5a78b7
docs/_build/html/analysis.html
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Analyzing and Modifying the PRESCOTT Output &mdash; esgemme 1.4.0 documentation</title>
<title>Analyzing and Modifying the PRESCOTT Output &mdash; prescott 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......@@ -32,7 +32,7 @@
<a href="index.html" class="icon icon-home">
esgemme
prescott
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
......@@ -46,7 +46,7 @@
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using PRESCOTT via Docker</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Analyzing and Modifying the PRESCOTT Output</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#raw-esgemme-scores-and-their-interpretation">Raw PRESCOTT Scores and Their Interpretation</a></li>
<li class="toctree-l2"><a class="reference internal" href="#raw-prescott-scores-and-their-interpretation">Raw PRESCOTT Scores and Their Interpretation</a></li>
<li class="toctree-l2"><a class="reference internal" href="#entire-single-point-mutation-landscape-calculations">Entire Single Point Mutation Landscape Calculations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#selected-single-point-or-multiple-point-mutation-calculations">Selected Single Point or Multiple Point Mutation Calculations</a></li>
</ul>
......@@ -61,7 +61,7 @@
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">esgemme</a>
<a href="index.html">prescott</a>
</nav>
<div class="wy-nav-content">
......@@ -79,10 +79,10 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<section id="analyzing-and-modifying-the-esgemme-output">
<h1>Analyzing and Modifying the PRESCOTT Output<a class="headerlink" href="#analyzing-and-modifying-the-esgemme-output" title="Permalink to this heading"></a></h1>
<section id="raw-esgemme-scores-and-their-interpretation">
<h2>Raw PRESCOTT Scores and Their Interpretation<a class="headerlink" href="#raw-esgemme-scores-and-their-interpretation" title="Permalink to this heading"></a></h2>
<section id="analyzing-and-modifying-the-prescott-output">
<h1>Analyzing and Modifying the PRESCOTT Output<a class="headerlink" href="#analyzing-and-modifying-the-prescott-output" title="Permalink to this heading"></a></h1>
<section id="raw-prescott-scores-and-their-interpretation">
<h2>Raw PRESCOTT Scores and Their Interpretation<a class="headerlink" href="#raw-prescott-scores-and-their-interpretation" title="Permalink to this heading"></a></h2>
<p>There is not a hardcoded limit for raw PRESCOTT scores. However, the values
range between [-12, 2] generally. The lower values mean the mutations is impactful,
while values close to 0 means the mutation does not have any significant impact.</p>
......
docs/_build/html/docker.html
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Using PRESCOTT via Docker &mdash; esgemme 1.4.0 documentation</title>
<title>Using PRESCOTT via Docker &mdash; prescott 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......@@ -32,7 +32,7 @@
<a href="index.html" class="icon icon-home">
esgemme
prescott
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
......@@ -67,7 +67,7 @@
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">esgemme</a>
<a href="index.html">prescott</a>
</nav>
<div class="wy-nav-content">
......@@ -85,8 +85,8 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<section id="using-esgemme-via-docker">
<h1>Using PRESCOTT via Docker<a class="headerlink" href="#using-esgemme-via-docker" title="Permalink to this heading"></a></h1>
<section id="using-prescott-via-docker">
<h1>Using PRESCOTT via Docker<a class="headerlink" href="#using-prescott-via-docker" title="Permalink to this heading"></a></h1>
<section id="requirements">
<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this heading"></a></h2>
<p>You need to have docker installed on your machine. You can consult the
......
docs/_build/html/genindex.html
......@@ -3,7 +3,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Index &mdash; esgemme 1.4.0 documentation</title>
<title>Index &mdash; prescott 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......@@ -29,7 +29,7 @@
<a href="index.html" class="icon icon-home">
esgemme
prescott
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
......@@ -53,7 +53,7 @@
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">esgemme</a>
<a href="index.html">prescott</a>
</nav>
<div class="wy-nav-content">
......
docs/_build/html/index.html
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Welcome to esgemme’s documentation! &mdash; esgemme 1.4.0 documentation</title>
<title>Welcome to esgemme’s documentation! &mdash; prescott 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......@@ -31,7 +31,7 @@
<a href="#" class="icon icon-home">
esgemme
prescott
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
......@@ -55,7 +55,7 @@
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="#">esgemme</a>
<a href="#">prescott</a>
</nav>
<div class="wy-nav-content">
......@@ -87,7 +87,7 @@
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the PRESCOTT Output</a><ul>
<li class="toctree-l2"><a class="reference internal" href="analysis.html#raw-esgemme-scores-and-their-interpretation">Raw PRESCOTT Scores and Their Interpretation</a></li>
<li class="toctree-l2"><a class="reference internal" href="analysis.html#raw-prescott-scores-and-their-interpretation">Raw PRESCOTT Scores and Their Interpretation</a></li>
<li class="toctree-l2"><a class="reference internal" href="analysis.html#entire-single-point-mutation-landscape-calculations">Entire Single Point Mutation Landscape Calculations</a></li>
<li class="toctree-l2"><a class="reference internal" href="analysis.html#selected-single-point-or-multiple-point-mutation-calculations">Selected Single Point or Multiple Point Mutation Calculations</a></li>
</ul>
......@@ -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#preparation-of-the-environment-and-installation-of-esgemme">Preparation of the environment and installation of PRESCOTT</a></li>
<li class="toctree-l2"><a class="reference internal" href="installation.html#preparation-of-the-environment-and-installation-of-prescott">Preparation of the environment and installation of PRESCOTT</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
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Preparing Your Own Input &mdash; esgemme 1.4.0 documentation</title>
<title>Preparing Your Own Input &mdash; prescott 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......@@ -32,7 +32,7 @@
<a href="index.html" class="icon icon-home">
esgemme
prescott
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
......@@ -59,7 +59,7 @@
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">esgemme</a>
<a href="index.html">prescott</a>
</nav>
<div class="wy-nav-content">
......
docs/_build/html/installation.html
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Installation &mdash; esgemme 1.4.0 documentation</title>
<title>Installation &mdash; prescott 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......@@ -31,7 +31,7 @@
<a href="index.html" class="icon icon-home">
esgemme
prescott
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
......@@ -48,7 +48,7 @@
<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="#preparation-of-the-environment-and-installation-of-esgemme">Preparation of the environment and installation of PRESCOTT</a></li>
<li class="toctree-l2"><a class="reference internal" href="#preparation-of-the-environment-and-installation-of-prescott">Preparation of the environment and installation of PRESCOTT</a></li>
<li class="toctree-l2"><a class="reference internal" href="#configuring-default-conf-file">Configuring default.conf file</a></li>
</ul>
</li>
......@@ -60,7 +60,7 @@
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">esgemme</a>
<a href="index.html">prescott</a>
</nav>
<div class="wy-nav-content">
......@@ -111,8 +111,8 @@ You can open .profile as follows:</p>
</div>
<p>JET2 is essential and it should be installed to be able to use PRESCOTT.</p>
</section>
<section id="preparation-of-the-environment-and-installation-of-esgemme">
<h2>Preparation of the environment and installation of PRESCOTT<a class="headerlink" href="#preparation-of-the-environment-and-installation-of-esgemme" title="Permalink to this heading"></a></h2>
<section id="preparation-of-the-environment-and-installation-of-prescott">
<h2>Preparation of the environment and installation of PRESCOTT<a class="headerlink" href="#preparation-of-the-environment-and-installation-of-prescott" 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>
......
docs/_build/html/search.html
......@@ -3,7 +3,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Search &mdash; esgemme 1.4.0 documentation</title>
<title>Search &mdash; prescott 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
......@@ -32,7 +32,7 @@
<a href="index.html" class="icon icon-home">
esgemme
prescott
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="#" method="get">
......@@ -56,7 +56,7 @@
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">esgemme</a>
<a href="index.html">prescott</a>
</nav>
<div class="wy-nav-content">
......
docs/_build/html/searchindex.js
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\ No newline at end of file
docs/_build/latex/esgemme.ilg deleted 100644 → 0
This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support).
Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored).
Scanning input file esgemme.idx...done (0 entries accepted, 0 rejected).
Nothing written in esgemme.ind.
Transcript written in esgemme.ilg.
docs/_build/latex/esgemme.aux → docs/_build/latex/prescott.aux
......@@ -23,7 +23,7 @@
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......@@ -42,10 +42,10 @@
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......@@ -65,7 +65,7 @@
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......
docs/_build/latex/esgemme.fdb_latexmk → docs/_build/latex/prescott.fdb_latexmk
# Fdb version 3
["makeindex esgemme.idx"] 1685453958 "esgemme.idx" "esgemme.ind" "esgemme" 1690888279
"esgemme.idx" 1690888279 0 d41d8cd98f00b204e9800998ecf8427e "pdflatex"
["makeindex prescott.idx"] 1691770116 "prescott.idx" "prescott.ind" "prescott" 1691770117
"prescott.idx" 1691770117 0 d41d8cd98f00b204e9800998ecf8427e "pdflatex"
(generated)
"esgemme.ilg"
"esgemme.ind"
["pdflatex"] 1690888278 "esgemme.tex" "esgemme.pdf" "esgemme" 1690888279
"prescott.ilg"
"prescott.ind"
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......@@ -138,37 +138,37 @@
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"prescott.aux"
"prescott.idx"
"prescott.log"
"prescott.out"
"prescott.pdf"
"prescott.toc"
docs/_build/latex/esgemme.fls → docs/_build/latex/prescott.fls
......@@ -3,8 +3,8 @@ INPUT /etc/texmf/web2c/texmf.cnf
INPUT /usr/share/texmf/web2c/texmf.cnf
INPUT /usr/share/texlive/texmf-dist/web2c/texmf.cnf
INPUT /var/lib/texmf/web2c/pdftex/pdflatex.fmt
INPUT esgemme.tex
OUTPUT esgemme.log
INPUT prescott.tex
OUTPUT prescott.log
INPUT ./sphinxmanual.cls
INPUT ./sphinxmanual.cls
INPUT sphinxmanual.cls
......@@ -82,7 +82,7 @@ INPUT /usr/share/texlive/texmf-dist/fonts/map/fontname/texfonts.map
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/jknappen/ec/ecrm1000.tfm
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INPUT /usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
......@@ -920,7 +920,7 @@ INPUT ./sphinxmessages.sty
INPUT sphinxmessages.sty
INPUT ./sphinxmessages.sty
INPUT sphinxmessages.sty
OUTPUT esgemme.idx
OUTPUT prescott.idx
INPUT /usr/share/texmf/tex/latex/tex-gyre/t1qtm.fd
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......@@ -937,10 +937,10 @@ INPUT /usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def
INPUT /usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def
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INPUT ./prescott.aux
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......@@ -998,17 +998,17 @@ INPUT /usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.st
INPUT /usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty
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INPUT ./prescott.out
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INPUT ./prescott.out
INPUT prescott.out
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INPUT prescott.out
INPUT ./prescott.out
INPUT prescott.out
INPUT ./prescott.out
INPUT ./prescott.out
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INPUT /usr/share/texmf/tex/latex/tex-gyre/t1qhv.fd
......@@ -1058,9 +1058,9 @@ INPUT /var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map
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INPUT ./esgemme.toc
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INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/cmextra/cmex7.tfm
......@@ -1068,7 +1068,7 @@ INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msam7.tfm
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OUTPUT esgemme.toc
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......@@ -1090,13 +1090,13 @@ INPUT /usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
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INPUT ./esgemme.ind
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......
docs/_build/latex/prescott.ilg 0 → 100644
This is makeindex, version 2.15 [TeX Live 2022/dev] (kpathsea + Thai support).
Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored).
Scanning input file prescott.idx...done (0 entries accepted, 0 rejected).
Nothing written in prescott.ind.
Transcript written in prescott.ilg.
docs/_build/latex/esgemme.log → docs/_build/latex/prescott.log
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.6.16) 1 AUG 2023 13:11
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.8.3) 11 AUG 2023 18:08
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
**esgemme.tex
(./esgemme.tex
**prescott.tex
(./prescott.tex
LaTeX2e <2021-11-15> patch level 1
L3 programming layer <2022-01-21> (./sphinxmanual.cls
Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual)
......@@ -118,7 +118,7 @@ LaTeX Font Info: Overwriting math alphabet `\mathfrak' in version `bold'
Package: babel 2022/01/26 3.70 The Babel package
\babel@savecnt=\count272
\U@D=\dimen148
\l@unhyphenated=\language3
\l@unhyphenated=\language9
(/usr/share/texlive/texmf-dist/tex/generic/babel/txtbabel.def)
\bbl@readstream=\read2
......@@ -126,16 +126,12 @@ Package: babel 2022/01/26 3.70 The Babel package
(/usr/share/texlive/texmf-dist/tex/generic/babel-english/english.ldf
Language: english 2017/06/06 v3.3r English support from the babel system
Package babel Info: Hyphen rules for 'british' set to \l@english
(babel) (\language0). Reported on input line 82.
Package babel Info: Hyphen rules for 'UKenglish' set to \l@english
(babel) (\language0). Reported on input line 83.
Package babel Info: Hyphen rules for 'canadian' set to \l@english
(babel) (\language0). Reported on input line 102.
Package babel Info: Hyphen rules for 'australian' set to \l@english
(babel) (\language0). Reported on input line 105.
Package babel Info: Hyphen rules for 'newzealand' set to \l@english
(babel) (\language0). Reported on input line 108.
Package babel Info: Hyphen rules for 'australian' set to \l@ukenglish
(babel) (\language3). Reported on input line 105.
Package babel Info: Hyphen rules for 'newzealand' set to \l@ukenglish
(babel) (\language3). Reported on input line 108.
))
(/usr/share/texmf/tex/latex/tex-gyre/tgtermes.sty
Package: tgtermes 2009/09/27 v1.2 TeX Gyre Termes as default roman family
......@@ -633,10 +629,10 @@ Package: hypcap 2016/05/16 v1.12 Adjusting the anchors of captions (HO)
Package: sphinxmessages 2019/01/04 v2.0 Localized LaTeX macros (Sphinx team)
)
\@indexfile=\write4
\openout4 = `esgemme.idx'.
\openout4 = `prescott.idx'.
Writing index file esgemme.idx
Writing index file prescott.idx
LaTeX Font Info: Trying to load font information for T1+qtm on input line 70
.
(/usr/share/texmf/tex/latex/tex-gyre/t1qtm.fd
......@@ -647,8 +643,8 @@ File: l3backend-pdftex.def 2022-01-12 L3 backend support: PDF output (pdfTeX)
\l__color_backend_stack_int=\count313
\l__pdf_internal_box=\box117
)
(./esgemme.aux)
\openout1 = `esgemme.aux'.
(./prescott.aux)
\openout1 = `prescott.aux'.
LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 70.
LaTeX Font Info: ... okay on input line 70.
......@@ -743,9 +739,9 @@ LaTeX Info: Redefining \ref on input line 70.
LaTeX Info: Redefining \pageref on input line 70.
LaTeX Info: Redefining \nameref on input line 70.
(./esgemme.out) (./esgemme.out)
(./prescott.out) (./prescott.out)
\@outlinefile=\write5
\openout5 = `esgemme.out'.
\openout5 = `prescott.out'.
Package hyperref Info: Option `pageanchor' set `false' on input line 78.
LaTeX Font Info: Trying to load font information for T1+qhv on input line 78
......@@ -769,9 +765,9 @@ File: umsb.fd 2013/01/14 v3.01 AMS symbols B
{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2
] (./esgemme.toc)
] (./prescott.toc)
\tf@toc=\write6
\openout6 = `esgemme.toc'.
\openout6 = `prescott.toc'.
[1
......@@ -808,7 +804,7 @@ LaTeX Font Info: Font shape `T1/txtt/m/it' in size <10> not available
Underfull \hbox (badness 10000) in paragraph at lines 456--460
[]\T1/qtm/m/n/10 Con-grat-u-la-tions! Now, you have all the in-put files re-qui
red for ES-GEMME: I. An in-put MSA:
red for PRESCOTT: I. An in-put MSA:
[]
[8]
......@@ -819,22 +815,28 @@ LaTeX Font Info: Trying to load font information for TS1+qtm on input line 4
File: ts1qtm.fd 2009/09/25 v1.2 font definition file for TS1/qtm
) [9
] [10] [11] [12
] [10]
Underfull \hbox (badness 7981) in paragraph at lines 627--630
[]\T1/qtm/m/n/10 #Down-load PRESCOTT from [][]$http : / / gitlab . lcqb . upmc
. fr / tekpinar / PRESCOTT$[][] repos-i-tory and go in-side the
[]
[11] [12
]
Chapter 5.
(./esgemme.ind) [13] (./esgemme.aux)
Package rerunfilecheck Info: File `esgemme.out' has not changed.
(rerunfilecheck) Checksum: 484D3D84B85998E14AB085F1C3F73044;4691.
(./prescott.ind) [13] (./prescott.aux)
Package rerunfilecheck Info: File `prescott.out' has not changed.
(rerunfilecheck) Checksum: C9F2E773136E992E346F95C229B25C19;4711.
)
Here is how much of TeX's memory you used:
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82 hyphenation exceptions out of 8191
70i,11n,76p,433b,568s stack positions out of 5000i,500n,10000p,200000b,80000s
{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}{/usr/share/texmf/fonts/
enc/dvips/tex-gyre/q-ec.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmmi5.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts
......@@ -845,7 +847,7 @@ usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt.pfb></usr/share/
texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/tex
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ts/type1/public/txfonts/tcxtt.pfb>
Output written on esgemme.pdf (17 pages, 164815 bytes).
Output written on prescott.pdf (17 pages, 164980 bytes).
PDF statistics:
259 PDF objects out of 1000 (max. 8388607)
220 compressed objects within 3 object streams
......
docs/_build/latex/esgemme.out → docs/_build/latex/prescott.out
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......@@ -6,14 +6,14 @@
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docs/_build/latex/esgemme.tex → docs/_build/latex/prescott.tex
......@@ -60,8 +60,8 @@
\title{esgemme}
\date{Aug 01, 2023}
\title{prescott}
\date{Aug 11, 2023}
\release{1.4.0}
\author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}}
......@@ -86,7 +86,7 @@
\chapter{Using PRESCOTT via Docker}
\label{\detokenize{docker:using-esgemme-via-docker}}\label{\detokenize{docker::doc}}
\label{\detokenize{docker:using-prescott-via-docker}}\label{\detokenize{docker::doc}}
\section{Requirements}
\label{\detokenize{docker:requirements}}
......@@ -259,10 +259,10 @@ mutation and its predicted effect, separated by a space.
\chapter{Analyzing and Modifying the PRESCOTT Output}
\label{\detokenize{analysis:analyzing-and-modifying-the-esgemme-output}}\label{\detokenize{analysis::doc}}
\label{\detokenize{analysis:analyzing-and-modifying-the-prescott-output}}\label{\detokenize{analysis::doc}}
\section{Raw PRESCOTT Scores and Their Interpretation}
\label{\detokenize{analysis:raw-esgemme-scores-and-their-interpretation}}
\label{\detokenize{analysis:raw-prescott-scores-and-their-interpretation}}
\sphinxAtStartPar
There is not a hardcoded limit for raw PRESCOTT scores. However, the values
range between {[}\sphinxhyphen{}12, 2{]} generally. The lower values mean the mutations is impactful,
......@@ -521,7 +521,7 @@ JET2 is essential and it should be installed to be able to use PRESCOTT.
\section{Preparation of the environment and installation of PRESCOTT}
\label{\detokenize{installation:preparation-of-the-environment-and-installation-of-esgemme}}
\label{\detokenize{installation:preparation-of-the-environment-and-installation-of-prescott}}
\sphinxAtStartPar
Step by step installation on Ubuntu 22.04
......
docs/conf.py
......@@ -18,7 +18,7 @@ sys.path.insert(0, os.path.abspath('../'))
import sphinx_rtd_theme
# -- Project information -----------------------------------------------------
project = 'esgemme'
project = 'prescott'
copyright = '2023, Mustafa Tekpinar'
author = 'Mustafa Tekpinar'
......
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