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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, 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. while values close to 0 means the mutation does not have any significant impact.
...@@ -13,7 +13,7 @@ it is not always the case. ...@@ -13,7 +13,7 @@ it is not always the case.
Entire Single Point Mutation Landscape Calculations 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*: and epistatic) scores*:
There are three output files: 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. sphinx-quickstart on Fri May 5 13:52:13 2023.
You can adapt this file completely to your liking, but it should at least You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive. contain the root `toctree` directive.
Welcome to esgemme's documentation! Welcome to PRESCOTT documentation!
=================================== ===================================
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
:caption: Contents: :caption: Contents:
introduction.rst
docker.rst docker.rst
analysis.rst analysis.rst
input-preparation.rst input-preparation.rst
......
docs/_build/html/analysis.html
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" /> <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
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<p class="caption" role="heading"><span class="caption-text">Contents:</span></p> <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current"> <ul class="current">
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using PRESCOTT via Docker</a></li> <li class="toctree-l1"><a class="reference internal" href="introduction.html"></a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Analyzing and Modifying the PRESCOTT Output</a><ul> <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-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#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="#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> <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> </ul>
...@@ -69,7 +72,7 @@ ...@@ -69,7 +72,7 @@
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<li class="breadcrumb-item active">Analyzing and Modifying the PRESCOTT Output</li> <li class="breadcrumb-item active">Analyzing and Modifying the ESCOTT Output</li>
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<div itemprop="articleBody"> <div itemprop="articleBody">
<section id="analyzing-and-modifying-the-prescott-output"> <section id="analyzing-and-modifying-the-escott-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> <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-prescott-scores-and-their-interpretation"> <section id="raw-escott-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> <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 PRESCOTT scores. However, the values <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, 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> 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 <p>We should note that most of the ‘impactful’ mutations are deleterious but
...@@ -91,7 +94,7 @@ it is not always the case.</p> ...@@ -91,7 +94,7 @@ it is not always the case.</p>
</section> </section>
<section id="entire-single-point-mutation-landscape-calculations"> <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> <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> and epistatic) scores*:</p>
<p>There are three output files:</p> <p>There are three output files:</p>
<ol class="arabic"> <ol class="arabic">
...@@ -143,7 +146,7 @@ D286F -0.23</p> ...@@ -143,7 +146,7 @@ D286F -0.23</p>
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu"> </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> <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul> <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="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="input-preparation.html">Preparing Your Own Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li> <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
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docs/_build/html/index.html
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" /> <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
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<p class="caption" role="heading"><span class="caption-text">Contents:</span></p> <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul> <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="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="input-preparation.html">Preparing Your Own Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li> <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
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...@@ -63,7 +64,7 @@ ...@@ -63,7 +64,7 @@
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<section id="welcome-to-esgemme-s-documentation"> <section id="welcome-to-prescott-documentation">
<h1>Welcome to esgemme’s documentation!<a class="headerlink" href="#welcome-to-esgemme-s-documentation" title="Permalink to this heading"></a></h1> <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"> <div class="toctree-wrapper compound">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p> <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul> <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>
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<li class="toctree-l2"><a class="reference internal" href="introduction.html#citation">Citation</a></li>
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<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a><ul> <li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a><ul>
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...@@ -86,8 +95,8 @@ ...@@ -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> <li class="toctree-l2"><a class="reference internal" href="docker.html#running-several-jobs-using-docker">Running several jobs using docker</a></li>
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<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the PRESCOTT Output</a><ul> <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-prescott-scores-and-their-interpretation">Raw PRESCOTT Scores and Their Interpretation</a></li> <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#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> <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>
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu"> </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> <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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<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="docker.html">Using ESCOTT via Docker</a></li>
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<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="input-preparation.html">Preparing Your Own Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li> <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
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docs/_build/latex/prescott.fdb_latexmk
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"/usr/share/texlive/texmf-dist/fonts/tfm/jknappen/ec/ecrm1000.tfm" 1136768653 3584 adb004a0c8e7c46ee66cad73671f37b4 "" "/usr/share/texlive/texmf-dist/fonts/tfm/jknappen/ec/ecrm1000.tfm" 1136768653 3584 adb004a0c8e7c46ee66cad73671f37b4 ""
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Chapter 1. Chapter 1.
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Chapter 2. Chapter 2.
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Chapter 3. Chapter 3.
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Chapter 4.
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Chapter 4. Chapter 5.
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Chapter 5. Chapter 6.
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docs/_build/latex/prescott.tex
...@@ -61,7 +61,7 @@ ...@@ -61,7 +61,7 @@
\title{prescott} \title{prescott}
\date{Sep 27, 2023} \date{Oct 10, 2023}
\release{1.5.0} \release{1.5.0}
\author{Mustafa Tekpinar} \author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}} \newcommand{\sphinxlogo}{\vbox{}}
...@@ -85,6 +85,168 @@ ...@@ -85,6 +85,168 @@
\sphinxstepscope \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} \chapter{Using ESCOTT via Docker}
\label{\detokenize{docker:using-escott-via-docker}}\label{\detokenize{docker::doc}} \label{\detokenize{docker:using-escott-via-docker}}\label{\detokenize{docker::doc}}
...@@ -258,13 +420,13 @@ mutation and its predicted effect, separated by a space. ...@@ -258,13 +420,13 @@ mutation and its predicted effect, separated by a space.
\sphinxstepscope \sphinxstepscope
\chapter{Analyzing and Modifying the PRESCOTT Output} \chapter{Analyzing and Modifying the ESCOTT Output}
\label{\detokenize{analysis:analyzing-and-modifying-the-prescott-output}}\label{\detokenize{analysis::doc}} \label{\detokenize{analysis:analyzing-and-modifying-the-escott-output}}\label{\detokenize{analysis::doc}}
\section{Raw PRESCOTT Scores and Their Interpretation} \section{Raw ESCOTT Scores and Their Interpretation}
\label{\detokenize{analysis:raw-prescott-scores-and-their-interpretation}} \label{\detokenize{analysis:raw-escott-scores-and-their-interpretation}}
\sphinxAtStartPar \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, 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. while values close to 0 means the mutation does not have any significant impact.
...@@ -276,7 +438,7 @@ it is not always the case. ...@@ -276,7 +438,7 @@ it is not always the case.
\section{Entire Single Point Mutation Landscape Calculations} \section{Entire Single Point Mutation Landscape Calculations}
\label{\detokenize{analysis:entire-single-point-mutation-landscape-calculations}} \label{\detokenize{analysis:entire-single-point-mutation-landscape-calculations}}
\sphinxAtStartPar \sphinxAtStartPar
By default, PRESCOTT will only output the combined (independent By default, ESCOTT will only output the combined (independent
and epistatic) scores*: and epistatic) scores*:
\sphinxAtStartPar \sphinxAtStartPar
......
docs/_build/latex/prescott.toc
\babel@toc {english}{}\relax \babel@toc {english}{}\relax
\contentsline {chapter}{\numberline {1}Using ESCOTT via Docker}{1}{chapter.1}% \contentsline {chapter}{\numberline {1}Introduction}{1}{chapter.1}%
\contentsline {section}{\numberline {1.1}Requirements}{1}{section.1.1}% \contentsline {section}{\numberline {1.1}What is PRESCOTT?}{1}{section.1.1}%
\contentsline {section}{\numberline {1.2}Getting the example input data}{1}{section.1.2}% \contentsline {section}{\numberline {1.2}Input Data Requirements}{1}{section.1.2}%
\contentsline {section}{\numberline {1.3}Single point mutation calculations}{2}{section.1.3}% \contentsline {subsection}{\numberline {1.2.1}Input Data Requirements for escott}{1}{subsection.1.2.1}%
\contentsline {subsection}{\numberline {1.3.1}Obtaining the entire single point mutation landscape}{2}{subsection.1.3.1}% \contentsline {subsection}{\numberline {1.2.2}Input Data Requirements for prescott}{2}{subsection.1.2.2}%
\contentsline {subsection}{\numberline {1.3.2}Predicting the effect of a subset of single point mutations}{2}{subsection.1.3.2}% \contentsline {section}{\numberline {1.3}Usage}{2}{section.1.3}%
\contentsline {section}{\numberline {1.4}Multiple point mutation calculations}{3}{section.1.4}% \contentsline {subsection}{\numberline {1.3.1}Running the escott program}{2}{subsection.1.3.1}%
\contentsline {section}{\numberline {1.5}Running several jobs using docker}{3}{section.1.5}% \contentsline {subsection}{\numberline {1.3.2}Running the prescott program}{2}{subsection.1.3.2}%
\contentsline {chapter}{\numberline {2}Analyzing and Modifying the PRESCOTT Output}{5}{chapter.2}% \contentsline {section}{\numberline {1.4}Installation}{3}{section.1.4}%
\contentsline {section}{\numberline {2.1}Raw PRESCOTT Scores and Their Interpretation}{5}{section.2.1}% \contentsline {section}{\numberline {1.5}Citation}{3}{section.1.5}%
\contentsline {section}{\numberline {2.2}Entire Single Point Mutation Landscape Calculations}{5}{section.2.2}% \contentsline {chapter}{\numberline {2}Using ESCOTT via Docker}{5}{chapter.2}%
\contentsline {section}{\numberline {2.3}Selected Single Point or Multiple Point Mutation Calculations}{6}{section.2.3}% \contentsline {section}{\numberline {2.1}Requirements}{5}{section.2.1}%
\contentsline {chapter}{\numberline {3}Preparing Your Own Input}{7}{chapter.3}% \contentsline {section}{\numberline {2.2}Getting the example input data}{5}{section.2.2}%
\contentsline {section}{\numberline {3.1}Preparing Your Input MSA and PDB with Colabfold}{7}{section.3.1}% \contentsline {section}{\numberline {2.3}Single point mutation calculations}{6}{section.2.3}%
\contentsline {chapter}{\numberline {4}Installation}{9}{chapter.4}% \contentsline {subsection}{\numberline {2.3.1}Obtaining the entire single point mutation landscape}{6}{subsection.2.3.1}%
\contentsline {section}{\numberline {4.1}Installing the dependencies:}{9}{section.4.1}% \contentsline {subsection}{\numberline {2.3.2}Predicting the effect of a subset of single point mutations}{6}{subsection.2.3.2}%
\contentsline {section}{\numberline {4.2}Preparation of the environment and installation of PRESCOTT}{9}{section.4.2}% \contentsline {section}{\numberline {2.4}Multiple point mutation calculations}{7}{section.2.4}%
\contentsline {section}{\numberline {4.3}Configuring default.conf file}{11}{section.4.3}% \contentsline {section}{\numberline {2.5}Running several jobs using docker}{7}{section.2.5}%
\contentsline {chapter}{\numberline {5}Indices and tables}{13}{chapter.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, 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. while values close to 0 means the mutation does not have any significant impact.
...@@ -13,7 +13,7 @@ it is not always the case. ...@@ -13,7 +13,7 @@ it is not always the case.
Entire Single Point Mutation Landscape Calculations 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*: and epistatic) scores*:
There are three output files: 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. sphinx-quickstart on Fri May 5 13:52:13 2023.
You can adapt this file completely to your liking, but it should at least You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive. contain the root `toctree` directive.
Welcome to esgemme's documentation! Welcome to PRESCOTT documentation!
=================================== ===================================
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
:caption: Contents: :caption: Contents:
introduction.rst
docker.rst docker.rst
analysis.rst analysis.rst
input-preparation.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
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