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docs/_build/html/_sources/docker.rst.txt
Using PRESCOTT via Docker
Using ESCOTT via Docker
========================
Requirements
......@@ -60,7 +60,7 @@ you may not need ‘sudo’ word before the docker command at all.
.. code:: bash
sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample \
tekpinar/esgemme-docker:v1.4.0
tekpinar/prescott-docker:v1.5.0
You are in the container (your virtual operating system) now. You
created a folder called myexample in your container with the previous
......@@ -81,7 +81,7 @@ In this step, we will use only evolutionary information from an MSA file:
.. code:: bash
esgemme aliBLAT.fasta -f aliBLAT.fasta
escott aliBLAT.fasta -f aliBLAT.fasta
After a few minutes of calculation, you must see at least two files named
BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
......@@ -93,7 +93,7 @@ evolutionary information:
.. code:: bash
esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
Predicting the effect of a subset of single point mutations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
......@@ -111,13 +111,13 @@ structural information. First, let's do it without structural information:
.. code:: bash
esgemme aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
escott aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way:
.. code:: bash
esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb \
escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb \
-m Stiffler_2015_BLAT_ECOLX.mut
You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output
......@@ -127,7 +127,7 @@ In addition, you won't have a png file like in the previous case.
Multiple point mutation calculations
------------------------------------
Sometimes, we need to see effects of double or triple mutations. PRESCOTT can
Sometimes, we need to see effects of double or triple mutations. ESCOTT can
perform calculations if you provide a mut file. In this case, the mut file must
have the following format:
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Analyzing and Modifying the PRESCOTT Output &mdash; prescott 1.4.0 documentation</title>
<title>Analyzing and Modifying the PRESCOTT Output &mdash; prescott 1.5.0 documentation</title>
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<title>Using PRESCOTT via Docker &mdash; prescott 1.4.0 documentation</title>
<title>Using ESCOTT via Docker &mdash; prescott 1.5.0 documentation</title>
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......@@ -44,7 +44,7 @@
</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 current"><a class="current reference internal" href="#">Using PRESCOTT via Docker</a><ul>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Using ESCOTT via Docker</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#requirements">Requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="#getting-the-example-input-data">Getting the example input data</a></li>
<li class="toctree-l2"><a class="reference internal" href="#single-point-mutation-calculations">Single point mutation calculations</a><ul>
......@@ -75,7 +75,7 @@
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<li class="breadcrumb-item active">Using PRESCOTT via Docker</li>
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......@@ -85,8 +85,8 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<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="using-escott-via-docker">
<h1>Using ESCOTT via Docker<a class="headerlink" href="#using-escott-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
......@@ -128,7 +128,7 @@ file in fasta format:</p>
<p>If it shows you a list of options, you are on a good track. On MacOS,
you may not need ‘sudo’ word before the docker command at all.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo docker run -ti --rm --mount <span class="nv">type</span><span class="o">=</span>bind,source<span class="o">=</span><span class="nv">$PWD</span>,target<span class="o">=</span>/home/tekpinar/research/myexample <span class="se">\</span>
tekpinar/esgemme-docker:v1.4.0
tekpinar/prescott-docker:v1.5.0
</pre></div>
</div>
<p>You are in the container (your virtual operating system) now. You
......@@ -144,7 +144,7 @@ docker container are pointing to the same place.</p>
<section id="obtaining-the-entire-single-point-mutation-landscape">
<h3>Obtaining the entire single point mutation landscape<a class="headerlink" href="#obtaining-the-entire-single-point-mutation-landscape" title="Permalink to this heading"></a></h3>
<p>In this step, we will use only evolutionary information from an MSA file:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>esgemme aliBLAT.fasta -f aliBLAT.fasta
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott aliBLAT.fasta -f aliBLAT.fasta
</pre></div>
</div>
<p>After a few minutes of calculation, you must see at least two files named
......@@ -153,7 +153,7 @@ the entire single point mutational landscape of BLAT protein in these
files.</p>
<p>If you want to utilize structural information (highly recommended) as well as
evolutionary information:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
</pre></div>
</div>
</section>
......@@ -168,11 +168,11 @@ Fortunately, we have an example mut in data folder of PRESCOTT repository.</p>
</div>
<p>Similar to the previous step, there are two possible ways to do the calculations: with or without
structural information. First, let’s do it without structural information:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>esgemme aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
</pre></div>
</div>
<p>You can include structural information in the following way:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb <span class="se">\</span>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb <span class="se">\</span>
-m Stiffler_2015_BLAT_ECOLX.mut
</pre></div>
</div>
......@@ -184,7 +184,7 @@ In addition, you won’t have a png file like in the previous case.</p>
</section>
<section id="multiple-point-mutation-calculations">
<h2>Multiple point mutation calculations<a class="headerlink" href="#multiple-point-mutation-calculations" title="Permalink to this heading"></a></h2>
<p>Sometimes, we need to see effects of double or triple mutations. PRESCOTT can
<p>Sometimes, we need to see effects of double or triple mutations. ESCOTT can
perform calculations if you provide a mut file. In this case, the mut file must
have the following format:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>E26D:Y44R
......
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......@@ -3,7 +3,7 @@
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<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="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="input-preparation.html">Preparing Your Own Input</a></li>
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\ No newline at end of file
docs/_build/latex/prescott.aux
......@@ -20,11 +20,11 @@
\providecommand\HyField@AuxAddToCoFields[2]{}
\babel@aux{english}{}
\newlabel{index::doc}{{}{1}{}{section*.2}{}}
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\@writefile{lof}{\addvspace {10\p@ }}
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\newlabel{docker::doc}{{1}{1}{Using PRESCOTT via Docker}{chapter.1}{}}
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\@writefile{toc}{\contentsline {section}{\numberline {1.2}Getting the example input data}{1}{section.1.2}\protected@file@percent }
......
docs/_build/latex/prescott.fdb_latexmk
# Fdb version 3
["makeindex prescott.idx"] 1691770116 "prescott.idx" "prescott.ind" "prescott" 1691770117
"prescott.idx" 1691770117 0 d41d8cd98f00b204e9800998ecf8427e "pdflatex"
["makeindex prescott.idx"] 1691770116 "prescott.idx" "prescott.ind" "prescott" 1695817598
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(generated)
"prescott.ilg"
"prescott.ind"
["pdflatex"] 1691770117 "prescott.tex" "prescott.pdf" "prescott" 1691770117
["pdflatex"] 1695817597 "prescott.tex" "prescott.pdf" "prescott" 1695817598
"/etc/texmf/web2c/texmf.cnf" 1686915816 475 c0e671620eb5563b2130f56340a5fde8 ""
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......
docs/_build/latex/prescott.log
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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
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......@@ -118,7 +118,7 @@ LaTeX Font Info: Overwriting math alphabet `\mathfrak' in version `bold'
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......@@ -129,9 +129,9 @@ Language: english 2017/06/06 v3.3r English support from the babel system
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Package: tgtermes 2009/09/27 v1.2 TeX Gyre Termes as default roman family
......@@ -827,15 +827,15 @@ Underfull \hbox (badness 7981) in paragraph at lines 627--630
Chapter 5.
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docs/_build/latex/prescott.out
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......
docs/_build/latex/prescott.tex
......@@ -61,8 +61,8 @@
\title{prescott}
\date{Aug 11, 2023}
\release{1.4.0}
\date{Sep 27, 2023}
\release{1.5.0}
\author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}}
\renewcommand{\releasename}{Release}
......@@ -85,8 +85,8 @@
\sphinxstepscope
\chapter{Using PRESCOTT via Docker}
\label{\detokenize{docker:using-prescott-via-docker}}\label{\detokenize{docker::doc}}
\chapter{Using ESCOTT via Docker}
\label{\detokenize{docker:using-escott-via-docker}}\label{\detokenize{docker::doc}}
\section{Requirements}
\label{\detokenize{docker:requirements}}
......@@ -155,7 +155,7 @@ you may not need ‘sudo’ word before the docker command at all.
\begin{sphinxVerbatim}[commandchars=\\\{\}]
sudo docker run \PYGZhy{}ti \PYGZhy{}\PYGZhy{}rm \PYGZhy{}\PYGZhy{}mount \PYG{n+nv}{type}\PYG{o}{=}bind,source\PYG{o}{=}\PYG{n+nv}{\PYGZdl{}PWD},target\PYG{o}{=}/home/tekpinar/research/myexample \PYG{l+s+se}{\PYGZbs{}}
tekpinar/esgemme\PYGZhy{}docker:v1.4.0
tekpinar/prescott\PYGZhy{}docker:v1.5.0
\end{sphinxVerbatim}
\sphinxAtStartPar
......@@ -180,7 +180,7 @@ docker container are pointing to the same place.
In this step, we will use only evolutionary information from an MSA file:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
esgemme aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta
escott aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta
\end{sphinxVerbatim}
\sphinxAtStartPar
......@@ -194,7 +194,7 @@ If you want to utilize structural information (highly recommended) as well as
evolutionary information:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
esgemme aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta \PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb
escott aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta \PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb
\end{sphinxVerbatim}
......@@ -215,14 +215,14 @@ Similar to the previous step, there are two possible ways to do the calculations
structural information. First, let’s do it without structural information:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
esgemme aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta \PYGZhy{}m Stiffler\PYGZus{}2015\PYGZus{}BLAT\PYGZus{}ECOLX.mut
escott aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta \PYGZhy{}m Stiffler\PYGZus{}2015\PYGZus{}BLAT\PYGZus{}ECOLX.mut
\end{sphinxVerbatim}
\sphinxAtStartPar
You can include structural information in the following way:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
esgemme aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta \PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb \PYG{l+s+se}{\PYGZbs{}}
escott aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta \PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb \PYG{l+s+se}{\PYGZbs{}}
\PYGZhy{}m Stiffler\PYGZus{}2015\PYGZus{}BLAT\PYGZus{}ECOLX.mut
\end{sphinxVerbatim}
......@@ -236,7 +236,7 @@ In addition, you won’t have a png file like in the previous case.
\section{Multiple point mutation calculations}
\label{\detokenize{docker:multiple-point-mutation-calculations}}
\sphinxAtStartPar
Sometimes, we need to see effects of double or triple mutations. PRESCOTT can
Sometimes, we need to see effects of double or triple mutations. ESCOTT can
perform calculations if you provide a mut file. In this case, the mut file must
have the following format:
......
docs/_build/latex/prescott.toc
\babel@toc {english}{}\relax
\contentsline {chapter}{\numberline {1}Using PRESCOTT via Docker}{1}{chapter.1}%
\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}%
......
docs/conf.py
......@@ -23,7 +23,7 @@ copyright = '2023, Mustafa Tekpinar'
author = 'Mustafa Tekpinar'
# The full version, including alpha/beta/rc tags
release = '1.4.0'
release = '1.5.0'
# -- General configuration ---------------------------------------------------
......
docs/docker.rst
Using PRESCOTT via Docker
Using ESCOTT via Docker
========================
Requirements
......@@ -60,7 +60,7 @@ you may not need ‘sudo’ word before the docker command at all.
.. code:: bash
sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample \
tekpinar/esgemme-docker:v1.4.0
tekpinar/prescott-docker:v1.5.0
You are in the container (your virtual operating system) now. You
created a folder called myexample in your container with the previous
......@@ -81,7 +81,7 @@ In this step, we will use only evolutionary information from an MSA file:
.. code:: bash
esgemme aliBLAT.fasta -f aliBLAT.fasta
escott aliBLAT.fasta -f aliBLAT.fasta
After a few minutes of calculation, you must see at least two files named
BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
......@@ -93,7 +93,7 @@ evolutionary information:
.. code:: bash
esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
Predicting the effect of a subset of single point mutations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
......@@ -111,13 +111,13 @@ structural information. First, let's do it without structural information:
.. code:: bash
esgemme aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
escott aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way:
.. code:: bash
esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb \
escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb \
-m Stiffler_2015_BLAT_ECOLX.mut
You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output
......@@ -127,7 +127,7 @@ In addition, you won't have a png file like in the previous case.
Multiple point mutation calculations
------------------------------------
Sometimes, we need to see effects of double or triple mutations. PRESCOTT can
Sometimes, we need to see effects of double or triple mutations. ESCOTT can
perform calculations if you provide a mut file. In this case, the mut file must
have the following format:
......
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