Skip to content

P
PRESCOTT
Commit e86e4bf6 by Mustafa Tekpinar
Options

Added introduction.rst and more documentation.

parent 42dbf51a
Showing with 437 additions and 116 deletions
docs/_build/html/_sources/analysis.rst.txt
Analyzing and Modifying the PRESCOTT Output
Analyzing and Modifying the ESCOTT Output
==========================================
Raw PRESCOTT Scores and Their Interpretation
Raw ESCOTT Scores and Their Interpretation
-------------------------------------------
There is not a hardcoded limit for raw PRESCOTT scores. However, the values
There is not a hardcoded limit for raw ESCOTT 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.
......@@ -13,7 +13,7 @@ it is not always the case.
Entire Single Point Mutation Landscape Calculations
---------------------------------------------------
By default, PRESCOTT will only output the combined (independent
By default, ESCOTT will only output the combined (independent
and epistatic) scores*:
There are three output files:
......
docs/_build/html/_sources/index.rst.txt
.. esgemme documentation master file, created by
.. PRESCOTT documentation master file, created by
sphinx-quickstart on Fri May 5 13:52:13 2023.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to esgemme's documentation!
Welcome to PRESCOTT documentation!
===================================
.. toctree::
:maxdepth: 2
:caption: Contents:
introduction.rst
docker.rst
analysis.rst
input-preparation.rst
......
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; prescott 1.5.0 documentation</title>
<title>Analyzing and Modifying the ESCOTT Output &mdash; prescott 1.5.0 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]>
......@@ -20,7 +20,7 @@
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Preparing Your Own Input" href="input-preparation.html" />
<link rel="prev" title="Using PRESCOTT via Docker" href="docker.html" />
<link rel="prev" title="Using ESCOTT via Docker" href="docker.html" />
</head>
<body class="wy-body-for-nav">
......@@ -44,9 +44,12 @@
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<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-prescott-scores-and-their-interpretation">Raw PRESCOTT Scores and Their Interpretation</a></li>
<li class="toctree-l1"><a class="reference internal" href="introduction.html"></a></li>
<li class="toctree-l1"><a class="reference internal" href="introduction.html#prescott-population-aware-epistatic-and-structural-model-of-mutational-effects">PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs</a></li>
<li class="toctree-l1"><a class="reference internal" href="introduction.html#cite">Cite</a></li>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Analyzing and Modifying the ESCOTT Output</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#raw-escott-scores-and-their-interpretation">Raw ESCOTT 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>
......@@ -69,7 +72,7 @@
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
<li class="breadcrumb-item active">Analyzing and Modifying the PRESCOTT Output</li>
<li class="breadcrumb-item active">Analyzing and Modifying the ESCOTT Output</li>
<li class="wy-breadcrumbs-aside">
<a href="_sources/analysis.rst.txt" rel="nofollow"> View page source</a>
</li>
......@@ -79,11 +82,11 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<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
<section id="analyzing-and-modifying-the-escott-output">
<h1>Analyzing and Modifying the ESCOTT Output<a class="headerlink" href="#analyzing-and-modifying-the-escott-output" title="Permalink to this heading"></a></h1>
<section id="raw-escott-scores-and-their-interpretation">
<h2>Raw ESCOTT Scores and Their Interpretation<a class="headerlink" href="#raw-escott-scores-and-their-interpretation" title="Permalink to this heading"></a></h2>
<p>There is not a hardcoded limit for raw ESCOTT 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>
<p>We should note that most of the ‘impactful’ mutations are deleterious but
......@@ -91,7 +94,7 @@ it is not always the case.</p>
</section>
<section id="entire-single-point-mutation-landscape-calculations">
<h2>Entire Single Point Mutation Landscape Calculations<a class="headerlink" href="#entire-single-point-mutation-landscape-calculations" title="Permalink to this heading"></a></h2>
<p>By default, PRESCOTT will only output the combined (independent
<p>By default, ESCOTT will only output the combined (independent
and epistatic) scores*:</p>
<p>There are three output files:</p>
<ol class="arabic">
......@@ -143,7 +146,7 @@ D286F -0.23</p>
</div>
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
<a href="docker.html" class="btn btn-neutral float-left" title="Using PRESCOTT via Docker" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
<a href="docker.html" class="btn btn-neutral float-left" title="Using ESCOTT via Docker" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
<a href="input-preparation.html" class="btn btn-neutral float-right" title="Preparing Your Own Input" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
</div>
......
docs/_build/html/genindex.html
......@@ -41,8 +41,9 @@
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the PRESCOTT Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT Output</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>
......
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; prescott 1.5.0 documentation</title>
<title>Welcome to PRESCOTT documentation! &mdash; prescott 1.5.0 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]>
......@@ -19,7 +19,7 @@
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Using ESCOTT via Docker" href="docker.html" />
<link rel="next" title="Introduction" href="introduction.html" />
</head>
<body class="wy-body-for-nav">
......@@ -43,8 +43,9 @@
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the PRESCOTT Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT Output</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>
......@@ -63,7 +64,7 @@
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
<li><a href="#" class="icon icon-home" aria-label="Home"></a></li>
<li class="breadcrumb-item active">Welcome to esgemme’s documentation!</li>
<li class="breadcrumb-item active">Welcome to PRESCOTT documentation!</li>
<li class="wy-breadcrumbs-aside">
<a href="_sources/index.rst.txt" rel="nofollow"> View page source</a>
</li>
......@@ -73,11 +74,19 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<section id="welcome-to-esgemme-s-documentation">
<h1>Welcome to esgemme’s documentation!<a class="headerlink" href="#welcome-to-esgemme-s-documentation" title="Permalink to this heading"></a></h1>
<section id="welcome-to-prescott-documentation">
<h1>Welcome to PRESCOTT documentation!<a class="headerlink" href="#welcome-to-prescott-documentation" title="Permalink to this heading"></a></h1>
<div class="toctree-wrapper compound">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a><ul>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#what-is-prescott">What is PRESCOTT?</a></li>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#input-data-requirements">Input Data Requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#usage">Usage</a></li>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#installation">Installation</a></li>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#citation">Citation</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a><ul>
<li class="toctree-l2"><a class="reference internal" href="docker.html#requirements">Requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="docker.html#getting-the-example-input-data">Getting the example input data</a></li>
......@@ -86,8 +95,8 @@
<li class="toctree-l2"><a class="reference internal" href="docker.html#running-several-jobs-using-docker">Running several jobs using docker</a></li>
</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-prescott-scores-and-their-interpretation">Raw PRESCOTT Scores and Their Interpretation</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT Output</a><ul>
<li class="toctree-l2"><a class="reference internal" href="analysis.html#raw-escott-scores-and-their-interpretation">Raw ESCOTT 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>
......@@ -118,7 +127,7 @@
</div>
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
<a href="docker.html" class="btn btn-neutral float-right" title="Using ESCOTT via Docker" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
<a href="introduction.html" class="btn btn-neutral float-right" title="Introduction" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
</div>
<hr/>
......
docs/_build/html/search.html
......@@ -44,8 +44,9 @@
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the PRESCOTT Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT Output</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>
......
docs/_build/latex/prescott.fdb_latexmk
# Fdb version 3
["makeindex prescott.idx"] 1691770116 "prescott.idx" "prescott.ind" "prescott" 1695817598
"prescott.idx" 1695817597 0 d41d8cd98f00b204e9800998ecf8427e "pdflatex"
["makeindex prescott.idx"] 1691770116 "prescott.idx" "prescott.ind" "prescott" 1696926737
"prescott.idx" 1696926737 0 d41d8cd98f00b204e9800998ecf8427e "pdflatex"
(generated)
"prescott.ilg"
"prescott.ind"
["pdflatex"] 1695817597 "prescott.tex" "prescott.pdf" "prescott" 1695817598
["pdflatex"] 1696926736 "prescott.tex" "prescott.pdf" "prescott" 1696926737
"/etc/texmf/web2c/texmf.cnf" 1686915816 475 c0e671620eb5563b2130f56340a5fde8 ""
"/usr/share/texlive/texmf-dist/fonts/map/fontname/texfonts.map" 1577235249 3524 cb3e574dea2d1052e39280babc910dc8 ""
"/usr/share/texlive/texmf-dist/fonts/tfm/jknappen/ec/ecrm1000.tfm" 1136768653 3584 adb004a0c8e7c46ee66cad73671f37b4 ""
......@@ -140,13 +140,13 @@
"/usr/share/texmf/web2c/texmf.cnf" 1644012257 39432 7155514e09a3d69036fac785183a21c2 ""
"/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map" 1692610720 128028 f533b797fba58d231669ea19e894e23e ""
"/var/lib/texmf/web2c/pdftex/pdflatex.fmt" 1692610730 1455466 cf5d347cc06e6f91065ccb2619b82e95 ""
"prescott.aux" 1695817597 6425 d4a0cc942c15d7d060b85f0f9e02b550 "pdflatex"
"prescott.aux" 1696926737 8757 49bd9be15e4a1990a75c401ccac48f11 "pdflatex"
"prescott.ind" 1694694190 0 d41d8cd98f00b204e9800998ecf8427e "makeindex prescott.idx"
"prescott.out" 1695817597 4701 4918ce853b06e7ffbb76675751d2708f "pdflatex"
"prescott.tex" 1695817596 25850 4bcc5c8c915860158ff9ba881b3f1df9 ""
"prescott.toc" 1695817597 1867 651c787e441d7670480cfc3502fbd769 "pdflatex"
"prescott.out" 1696926737 6307 8119393c8f110ffbb217a1e7b2c390de "pdflatex"
"prescott.tex" 1696926736 31550 20f37acb31b6833dc824f7480aecb279 ""
"prescott.toc" 1696926737 2706 6a2a8c488f73b27e9fedb6cddefdfa53 "pdflatex"
"sphinx.sty" 1691571542 12780 919e6ba449302e2597e7722681a087c6 ""
"sphinxhighlight.sty" 1695817596 6679 76d10c62e0f0661410b46f5db6118e26 ""
"sphinxhighlight.sty" 1696926736 6679 76d10c62e0f0661410b46f5db6118e26 ""
"sphinxlatexadmonitions.sty" 1691571543 6238 2d867d769abf3f72abc17ef52adff78b ""
"sphinxlatexcontainers.sty" 1691571543 901 d3a3a1b7b2547f47ade2499350b5c420 ""
"sphinxlatexgraphics.sty" 1691571543 4840 a9578332b6f3b35e198751fb632c9b79 ""
......@@ -161,7 +161,7 @@
"sphinxlatexstyletext.sty" 1691571543 6177 c18841ce3fafc366cd3b145f8faa4c37 ""
"sphinxlatextables.sty" 1691571542 21848 2827eb0b11b99b185a8b77317d3e131c ""
"sphinxmanual.cls" 1691571543 4241 7b0d7a37df7b5715fb0dbd585c52ecdb ""
"sphinxmessages.sty" 1695817596 745 3f5fcd6cdd7964ed608767954a8ced6f ""
"sphinxmessages.sty" 1696926736 745 3f5fcd6cdd7964ed608767954a8ced6f ""
"sphinxoptionsgeometry.sty" 1691571542 2061 47bb34b8ed8a78823eb0c886abfb9f4d ""
"sphinxoptionshyperref.sty" 1691571543 1094 79beb8b8a3f10784f8cce804e0f9d3aa ""
"sphinxpackagefootnote.sty" 1691571543 15217 dd26fe418b6fb1b26b18f042a7f43d40 ""
......
docs/_build/latex/prescott.fls
......@@ -1069,6 +1069,13 @@ INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msam5.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm7.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm5.tfm
OUTPUT prescott.toc
INPUT /usr/share/texmf/fonts/tfm/public/tex-gyre/ec-qtmr.tfm
INPUT /usr/share/texmf/fonts/tfm/public/tex-gyre/ec-qhvr.tfm
INPUT /usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
INPUT /usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
INPUT /usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
INPUT /usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
INPUT /usr/share/texmf/fonts/tfm/public/tex-gyre/ts1-qtmr.tfm
INPUT /usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd
INPUT /usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd
INPUT /usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd
......@@ -1076,19 +1083,12 @@ INPUT /usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/txfonts/t1xtt.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/txfonts/t1xtt.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/txfonts/t1xbtt.tfm
INPUT /usr/share/texmf/fonts/tfm/public/tex-gyre/ec-qtmr.tfm
INPUT /usr/share/texmf/fonts/tfm/public/tex-gyre/ec-qhvr.tfm
INPUT /usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd
INPUT /usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd
INPUT /usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd
INPUT /usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/txfonts/tcxtt.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/txfonts/t1xttsl.tfm
INPUT /usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
INPUT /usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
INPUT /usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
INPUT /usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
INPUT /usr/share/texmf/fonts/tfm/public/tex-gyre/ts1-qtmr.tfm
INPUT /usr/share/texmf/fonts/tfm/public/tex-gyre/ec-qtmr.tfm
INPUT ./prescott.ind
INPUT prescott.ind
......
docs/_build/latex/prescott.log
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.8.21) 27 SEP 2023 14:26
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.8.21) 10 OCT 2023 10:32
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
......@@ -775,68 +775,74 @@ File: umsb.fd 2013/01/14 v3.01 AMS symbols B
]
Chapter 1.
LaTeX Font Info: Trying to load font information for TS1+qtm on input line 1
15.
(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
File: ts1qtm.fd 2009/09/25 v1.2 font definition file for TS1/qtm
)
LaTeX Font Info: Trying to load font information for T1+txtt on input line 1
08.
21.
(/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd
File: t1txtt.fd 2000/12/15 v3.1
) [1
]
)
LaTeX Font Info: Font shape `T1/txtt/b/n' in size <10> not available
(Font) Font shape `T1/txtt/bx/n' tried instead on input line 157.
[2] [3]
(Font) Font shape `T1/txtt/bx/n' tried instead on input line 122.
[1
] [2] [3]
[4
]
Chapter 2.
[5] [6]
[5] [6] [7] [8
]
Chapter 3.
[7
[9] [10]
Chapter 4.
[11
]
LaTeX Font Info: Trying to load font information for TS1+txtt on input line
451.
613.
(/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd
File: ts1txtt.fd 2000/12/15 v3.1
)
LaTeX Font Info: Font shape `T1/txtt/m/it' in size <10> not available
(Font) Font shape `T1/txtt/m/sl' tried instead on input line 452.
(Font) Font shape `T1/txtt/m/sl' tried instead on input line 614.
Underfull \hbox (badness 10000) in paragraph at lines 456--460
Underfull \hbox (badness 10000) in paragraph at lines 618--622
[]\T1/qtm/m/n/10 Con-grat-u-la-tions! Now, you have all the in-put files re-qui
red for PRESCOTT: I. An in-put MSA:
[]
[8]
Chapter 4.
LaTeX Font Info: Trying to load font information for TS1+qtm on input line 4
78.
(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
File: ts1qtm.fd 2009/09/25 v1.2 font definition file for TS1/qtm
) [9
[12]
Chapter 5.
[13
] [10]
Underfull \hbox (badness 7981) in paragraph at lines 627--630
] [14]
Underfull \hbox (badness 7981) in paragraph at lines 789--792
[]\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
[15] [16
]
Chapter 5.
(./prescott.ind) [13] (./prescott.aux)
Chapter 6.
(./prescott.ind) [17] (./prescott.aux)
Package rerunfilecheck Info: File `prescott.out' has not changed.
(rerunfilecheck) Checksum: 4918CE853B06E7FFBB76675751D2708F;4701.
(rerunfilecheck) Checksum: 8119393C8F110FFBB217A1E7B2C390DE;6307.
)
Here is how much of TeX's memory you used:
14655 strings out of 480204
233351 string characters out of 5895010
597904 words of memory out of 5000000
32190 multiletter control sequences out of 15000+600000
14691 strings out of 480204
234048 string characters out of 5895010
598445 words of memory out of 5000000
32212 multiletter control sequences out of 15000+600000
520869 words of font info for 70 fonts, out of 8000000 for 9000
37 hyphenation exceptions out of 8191
70i,11n,76p,433b,568s stack positions out of 5000i,500n,10000p,200000b,80000s
70i,11n,76p,434b,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
......@@ -847,10 +853,10 @@ 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
mf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/txfonts/tcxtt.pfb>
Output written on prescott.pdf (17 pages, 165007 bytes).
Output written on prescott.pdf (21 pages, 172572 bytes).
PDF statistics:
259 PDF objects out of 1000 (max. 8388607)
220 compressed objects within 3 object streams
51 named destinations out of 1000 (max. 500000)
173 words of extra memory for PDF output out of 10000 (max. 10000000)
329 PDF objects out of 1000 (max. 8388607)
286 compressed objects within 3 object streams
65 named destinations out of 1000 (max. 500000)
253 words of extra memory for PDF output out of 10000 (max. 10000000)
docs/_build/latex/prescott.tex
......@@ -61,7 +61,7 @@
\title{prescott}
\date{Sep 27, 2023}
\date{Oct 10, 2023}
\release{1.5.0}
\author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}}
......@@ -85,6 +85,168 @@
\sphinxstepscope
\chapter{Introduction}
\label{\detokenize{introduction:introduction}}\label{\detokenize{introduction::doc}}
\section{What is PRESCOTT?}
\label{\detokenize{introduction:what-is-prescott}}
\sphinxAtStartPar
PRESCOTT (PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs) is a package predicting mutational effects in a protein based
on population, evolutionary and structural information. It is made up of
two main programs: escott and prescott.
\sphinxAtStartPar
ESCOTT can calculate effects of single point mutations and multiple
point mutations. On the other hand, PRESCOTT incorporates population
frequencies into ESCOTT predictions. Therefore, you need to run ESCOTT
first to have predictions of mutational effects. We recommend using
PRESCOTT package via our web site or our docker image due to its
dependencies.
\section{Input Data Requirements}
\label{\detokenize{introduction:input-data-requirements}}
\subsection{Input Data Requirements for escott}
\label{\detokenize{introduction:input-data-requirements-for-escott}}
\sphinxAtStartPar
escott requires two files:
\begin{itemize}
\item {}
\sphinxAtStartPar
a multiple sequence alignment (MSA) file in fasta format (mandatory):
\end{itemize}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{n}{Your} \PYG{n}{query} \PYG{n}{protein} \PYG{n}{must} \PYG{n}{be} \PYG{n}{the} \PYG{n}{first} \PYG{n}{sequence} \PYG{o+ow}{in} \PYG{n}{the} \PYG{n}{fasta} \PYG{n}{file}\PYG{o}{.} \PYG{n}{In} \PYG{n}{addition}\PYG{p}{,} \PYG{n}{the} \PYG{n}{query} \PYG{n}{sequence} \PYG{n}{should} \PYG{o+ow}{not} \PYG{n}{contain} \PYG{n+nb}{any} \PYG{n}{gaps}\PYG{o}{.}
\end{sphinxVerbatim}
\begin{itemize}
\item {}
\sphinxAtStartPar
a structure file in PDB format (optional but highly recommended).
\end{itemize}
\sphinxAtStartPar
One of the fastest ways to obtain both input MSA and a PDB file is to
run colabfold:
\sphinxurl{https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb}
\sphinxAtStartPar
Please note that the MSA file produced by colabfold (a3m file) can
contain gaps in the query sequence. You have to remove them before using
it in PRESCOTT. You can remove the gaps with pragrams that have a GUI,
such as ugene (\sphinxurl{http://ugene.net/}) or jalview (\sphinxurl{https://www.jalview.org/}).
\sphinxAtStartPar
For testing purpose, you can find some example input files for BLAT
protein in data/ folder of this repository.
\subsection{Input Data Requirements for prescott}
\label{\detokenize{introduction:input-data-requirements-for-prescott}}
\sphinxAtStartPar
prescott requires three files:
\begin{itemize}
\item {}
\sphinxAtStartPar
output file of escott (the file ending with …normPredCombi.txt)
\item {}
\sphinxAtStartPar
a fasta file containing only your query sequence
\item {}
\sphinxAtStartPar
gnomad csv file containing to be downloaded from \sphinxurl{https://gnomad.broadinstitute.org/} for your protein.
\end{itemize}
\section{Usage}
\label{\detokenize{introduction:usage}}
\sphinxAtStartPar
You can find example bash scripts for escott and prescott in examples
folder of this repository.
\sphinxAtStartPar
Below, you will find examples of the most basic usage. Consult to the
documentation for further details.
\subsection{Running the escott program}
\label{\detokenize{introduction:running-the-escott-program}}
\sphinxAtStartPar
Let’s assume that our input MSA is inputAli.fasta and input.pdb is our
structure file in PDB format.
\sphinxAtStartPar
Run the program by issuing the following command in a bash terminal:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
escott inputAli.fasta \PYGZhy{}f inputAli.fasta \PYGZhy{}\PYGZhy{}pdbfile input.pdb
\end{sphinxVerbatim}
\sphinxAtStartPar
A quick help can be accessed by typing
\begin{sphinxVerbatim}[commandchars=\\\{\}]
escott \PYGZhy{}\PYGZhy{}help
\end{sphinxVerbatim}
\sphinxAtStartPar
By default, ESCOTT will predict the effect of all possible single
mutations at all positions in the query sequence. Alternatively, a set
of single or multiple mutations can be given with the option \sphinxhyphen{}m. Each
line of the file should contain a mutation (e.g. D136R) or combination
of mutations separated by colons and ordered according to their
positions in the sequence (e.g. D136R,V271A).
\subsection{Running the prescott program}
\label{\detokenize{introduction:running-the-prescott-program}}
\sphinxAtStartPar
A quick help can be accessed by typing
\begin{sphinxVerbatim}[commandchars=\\\{\}]
prescott \PYGZhy{}\PYGZhy{}help
\end{sphinxVerbatim}
\sphinxAtStartPar
Run the program by issuing the following command in a bash terminal:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
prescott \PYGZhy{}e ../data/MLH1\PYGZus{}normPred\PYGZus{}evolCombi.txt \PYGZhy{}g ../data/gnomAD\PYGZus{}v2.1.1\PYGZus{}MLH1\PYGZus{}HUMAN\PYGZus{}ENSG00000076242.csv \PYGZhy{}s ../data/MLH1.fasta
\end{sphinxVerbatim}
\sphinxAtStartPar
The most important output is prescott\sphinxhyphen{}scores.txt file, which produces
frequecy modified scores for the mutations.
\sphinxAtStartPar
Please note that the example input files for prescott are in the data
directory of this repository.
\section{Installation}
\label{\detokenize{introduction:installation}}
\sphinxAtStartPar
PRESCOTT is implemented in Python 3 and R. It has been tested only on
Linux. Since PRESCOTT has many dependencies, we recommend using our web
site or our docker image. If you are a determined user, you can find the
steps required to install it from the source in the following link (or
in the docs folder of this repository):
\section{Citation}
\label{\detokenize{introduction:citation}}
\sphinxAtStartPar
Coming soon…
\sphinxstepscope
\chapter{Using ESCOTT via Docker}
\label{\detokenize{docker:using-escott-via-docker}}\label{\detokenize{docker::doc}}
......@@ -258,13 +420,13 @@ mutation and its predicted effect, separated by a space.
\sphinxstepscope
\chapter{Analyzing and Modifying the PRESCOTT Output}
\label{\detokenize{analysis:analyzing-and-modifying-the-prescott-output}}\label{\detokenize{analysis::doc}}
\chapter{Analyzing and Modifying the ESCOTT Output}
\label{\detokenize{analysis:analyzing-and-modifying-the-escott-output}}\label{\detokenize{analysis::doc}}
\section{Raw PRESCOTT Scores and Their Interpretation}
\label{\detokenize{analysis:raw-prescott-scores-and-their-interpretation}}
\section{Raw ESCOTT Scores and Their Interpretation}
\label{\detokenize{analysis:raw-escott-scores-and-their-interpretation}}
\sphinxAtStartPar
There is not a hardcoded limit for raw PRESCOTT scores. However, the values
There is not a hardcoded limit for raw ESCOTT scores. However, the values
range between {[}\sphinxhyphen{}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.
......@@ -276,7 +438,7 @@ it is not always the case.
\section{Entire Single Point Mutation Landscape Calculations}
\label{\detokenize{analysis:entire-single-point-mutation-landscape-calculations}}
\sphinxAtStartPar
By default, PRESCOTT will only output the combined (independent
By default, ESCOTT will only output the combined (independent
and epistatic) scores*:
\sphinxAtStartPar
......
docs/_build/latex/prescott.toc
\babel@toc {english}{}\relax
\contentsline {chapter}{\numberline {1}Using ESCOTT via Docker}{1}{chapter.1}%
\contentsline {section}{\numberline {1.1}Requirements}{1}{section.1.1}%
\contentsline {section}{\numberline {1.2}Getting the example input data}{1}{section.1.2}%
\contentsline {section}{\numberline {1.3}Single point mutation calculations}{2}{section.1.3}%
\contentsline {subsection}{\numberline {1.3.1}Obtaining the entire single point mutation landscape}{2}{subsection.1.3.1}%
\contentsline {subsection}{\numberline {1.3.2}Predicting the effect of a subset of single point mutations}{2}{subsection.1.3.2}%
\contentsline {section}{\numberline {1.4}Multiple point mutation calculations}{3}{section.1.4}%
\contentsline {section}{\numberline {1.5}Running several jobs using docker}{3}{section.1.5}%
\contentsline {chapter}{\numberline {2}Analyzing and Modifying the PRESCOTT Output}{5}{chapter.2}%
\contentsline {section}{\numberline {2.1}Raw PRESCOTT Scores and Their Interpretation}{5}{section.2.1}%
\contentsline {section}{\numberline {2.2}Entire Single Point Mutation Landscape Calculations}{5}{section.2.2}%
\contentsline {section}{\numberline {2.3}Selected Single Point or Multiple Point Mutation Calculations}{6}{section.2.3}%
\contentsline {chapter}{\numberline {3}Preparing Your Own Input}{7}{chapter.3}%
\contentsline {section}{\numberline {3.1}Preparing Your Input MSA and PDB with Colabfold}{7}{section.3.1}%
\contentsline {chapter}{\numberline {4}Installation}{9}{chapter.4}%
\contentsline {section}{\numberline {4.1}Installing the dependencies:}{9}{section.4.1}%
\contentsline {section}{\numberline {4.2}Preparation of the environment and installation of PRESCOTT}{9}{section.4.2}%
\contentsline {section}{\numberline {4.3}Configuring default.conf file}{11}{section.4.3}%
\contentsline {chapter}{\numberline {5}Indices and tables}{13}{chapter.5}%
\contentsline {chapter}{\numberline {1}Introduction}{1}{chapter.1}%
\contentsline {section}{\numberline {1.1}What is PRESCOTT?}{1}{section.1.1}%
\contentsline {section}{\numberline {1.2}Input Data Requirements}{1}{section.1.2}%
\contentsline {subsection}{\numberline {1.2.1}Input Data Requirements for escott}{1}{subsection.1.2.1}%
\contentsline {subsection}{\numberline {1.2.2}Input Data Requirements for prescott}{2}{subsection.1.2.2}%
\contentsline {section}{\numberline {1.3}Usage}{2}{section.1.3}%
\contentsline {subsection}{\numberline {1.3.1}Running the escott program}{2}{subsection.1.3.1}%
\contentsline {subsection}{\numberline {1.3.2}Running the prescott program}{2}{subsection.1.3.2}%
\contentsline {section}{\numberline {1.4}Installation}{3}{section.1.4}%
\contentsline {section}{\numberline {1.5}Citation}{3}{section.1.5}%
\contentsline {chapter}{\numberline {2}Using ESCOTT via Docker}{5}{chapter.2}%
\contentsline {section}{\numberline {2.1}Requirements}{5}{section.2.1}%
\contentsline {section}{\numberline {2.2}Getting the example input data}{5}{section.2.2}%
\contentsline {section}{\numberline {2.3}Single point mutation calculations}{6}{section.2.3}%
\contentsline {subsection}{\numberline {2.3.1}Obtaining the entire single point mutation landscape}{6}{subsection.2.3.1}%
\contentsline {subsection}{\numberline {2.3.2}Predicting the effect of a subset of single point mutations}{6}{subsection.2.3.2}%
\contentsline {section}{\numberline {2.4}Multiple point mutation calculations}{7}{section.2.4}%
\contentsline {section}{\numberline {2.5}Running several jobs using docker}{7}{section.2.5}%
\contentsline {chapter}{\numberline {3}Analyzing and Modifying the ESCOTT Output}{9}{chapter.3}%
\contentsline {section}{\numberline {3.1}Raw ESCOTT Scores and Their Interpretation}{9}{section.3.1}%
\contentsline {section}{\numberline {3.2}Entire Single Point Mutation Landscape Calculations}{9}{section.3.2}%
\contentsline {section}{\numberline {3.3}Selected Single Point or Multiple Point Mutation Calculations}{10}{section.3.3}%
\contentsline {chapter}{\numberline {4}Preparing Your Own Input}{11}{chapter.4}%
\contentsline {section}{\numberline {4.1}Preparing Your Input MSA and PDB with Colabfold}{11}{section.4.1}%
\contentsline {chapter}{\numberline {5}Installation}{13}{chapter.5}%
\contentsline {section}{\numberline {5.1}Installing the dependencies:}{13}{section.5.1}%
\contentsline {section}{\numberline {5.2}Preparation of the environment and installation of PRESCOTT}{13}{section.5.2}%
\contentsline {section}{\numberline {5.3}Configuring default.conf file}{15}{section.5.3}%
\contentsline {chapter}{\numberline {6}Indices and tables}{17}{chapter.6}%
docs/analysis.rst
Analyzing and Modifying the PRESCOTT Output
Analyzing and Modifying the ESCOTT Output
==========================================
Raw PRESCOTT Scores and Their Interpretation
Raw ESCOTT Scores and Their Interpretation
-------------------------------------------
There is not a hardcoded limit for raw PRESCOTT scores. However, the values
There is not a hardcoded limit for raw ESCOTT 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.
......@@ -13,7 +13,7 @@ it is not always the case.
Entire Single Point Mutation Landscape Calculations
---------------------------------------------------
By default, PRESCOTT will only output the combined (independent
By default, ESCOTT will only output the combined (independent
and epistatic) scores*:
There are three output files:
......
docs/index.rst
.. esgemme documentation master file, created by
.. PRESCOTT documentation master file, created by
sphinx-quickstart on Fri May 5 13:52:13 2023.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to esgemme's documentation!
Welcome to PRESCOTT documentation!
===================================
.. toctree::
:maxdepth: 2
:caption: Contents:
introduction.rst
docker.rst
analysis.rst
input-preparation.rst
......
docs/introduction.rst 0 → 100644
Introduction
============
What is PRESCOTT?
-----------------
PRESCOTT (PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs) is a package predicting mutational effects in a protein based
on population, evolutionary and structural information. It is made up of
two main programs: escott and prescott.
ESCOTT can calculate effects of single point mutations and multiple
point mutations. On the other hand, PRESCOTT incorporates population
frequencies into ESCOTT predictions. Therefore, you need to run ESCOTT
first to have predictions of mutational effects. We recommend using
PRESCOTT package via our web site or our docker image due to its
dependencies.
Input Data Requirements
-----------------------
Input Data Requirements for escott
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
escott requires two files:
* a multiple sequence alignment (MSA) file in fasta format (mandatory):
::
Your query protein must be the first sequence in the fasta file. In addition, the query sequence should not contain any gaps.
* a structure file in PDB format (optional but highly recommended).
One of the fastest ways to obtain both input MSA and a PDB file is to
run colabfold:
https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
Please note that the MSA file produced by colabfold (a3m file) can
contain gaps in the query sequence. You have to remove them before using
it in PRESCOTT. You can remove the gaps with pragrams that have a GUI,
such as ugene (http://ugene.net/) or jalview (https://www.jalview.org/).
For testing purpose, you can find some example input files for BLAT
protein in data/ folder of this repository.
Input Data Requirements for prescott
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
prescott requires three files:
* output file of escott (the file ending with …normPredCombi.txt)
* a fasta file containing only your query sequence
* gnomad csv file containing to be downloaded from https://gnomad.broadinstitute.org/ for your protein.
Usage
-----
You can find example bash scripts for escott and prescott in examples
folder of this repository.
Below, you will find examples of the most basic usage. Consult to the
documentation for further details.
Running the escott program
~~~~~~~~~~~~~~~~~~~~~~~~~~
Let’s assume that our input MSA is inputAli.fasta and input.pdb is our
structure file in PDB format.
Run the program by issuing the following command in a bash terminal:
.. code:: bash
escott inputAli.fasta -f inputAli.fasta --pdbfile input.pdb
A quick help can be accessed by typing
.. code:: bash
escott --help
By default, ESCOTT will predict the effect of all possible single
mutations at all positions in the query sequence. Alternatively, a set
of single or multiple mutations can be given with the option -m. Each
line of the file should contain a mutation (e.g. D136R) or combination
of mutations separated by colons and ordered according to their
positions in the sequence (e.g. D136R,V271A).
Running the prescott program
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
A quick help can be accessed by typing
.. code:: bash
prescott --help
Run the program by issuing the following command in a bash terminal:
.. code:: bash
prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v2.1.1_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta
The most important output is prescott-scores.txt file, which produces
frequecy modified scores for the mutations.
Please note that the example input files for prescott are in the data
directory of this repository.
Installation
------------
PRESCOTT is implemented in Python 3 and R. It has been tested only on
Linux. Since PRESCOTT has many dependencies, we recommend using our web
site or our docker image. If you are a determined user, you can find the
steps required to install it from the source in the following link (or
in the docs folder of this repository):
Citation
--------
Coming soon…
.. |License: MIT| image:: https://img.shields.io/badge/License-MIT-yellow.svg
:target: https://opensource.org/licenses/MIT
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment