Commit 21f4813c by Mustafa Tekpinar

If a pdbfile is provided, normweightmode becomes sstjetormaxtwocomponent…

If a pdbfile is provided, normweightmode becomes sstjetormaxtwocomponent automatically. Else, it is tjet.
parent 8603802b
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 22c71542c2e9339759d7f2af8f251cf8
config: fe2e7449c75c4a1331acfe403ef4e427
tags: 645f666f9bcd5a90fca523b33c5a78b7
......@@ -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:v1.3.0
tekpinar/esgemme-docker:v1.4.0
You are in the container (your virtual operating system) now. You
created a folder called myexample in your container with the previous
......@@ -94,8 +94,7 @@ evolutionary information:
.. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
--normweightmode sstjetormax
--pdbfile blat-af2.pdb
Predicting the effect of a subset of single point mutations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
......@@ -117,11 +116,11 @@ structural information. First, let's do it without structural information:
-m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way:
.. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
--normweightmode sstjetormax \
-m Stiffler_2015_BLAT_ECOLX.mut
You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output
......
......@@ -15,12 +15,30 @@ ESGEMME has the following external dependencies:
* java
* naccess: http://www.bioinf.manchester.ac.uk/naccess/
* muscle: https://www.drive5.com/muscle/
* seqinr R package: https://cran.r-project.org/web/packages/seqinr/index.html
* dssp for secondary structure prediction.
After you installed JET2 define a parameter called JET2_PATH inside your .profile file.
You can open .profile as follows:
These tools should be installed to be able to use ESGEMME.
.. code:: bash
gedit ~/.profile
You should add a command like below to the end of that file, save and exit.
.. code:: bash
export JET2_PATH=/home/tekpinar/JET2/
Please, do not forget to replace /home/tekpinar/JET2 with your own file path.
Then, source the saved .profile so that the environment variable will be taken into account:
.. code:: bash
source ~/.profile
JET2 is essential and it should be installed to be able to use ESGEMME.
Preparation of the environment and installation of ESGEMME
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
......@@ -54,13 +72,16 @@ Prepare your environment and install the required packages:
#Dssp installation
If you are using Ubuntu 20.04, you can install dssp by the following command
.. code:: bash
sudo apt-get install dssp
Otherwise, you can install it from the source by the following commands.
Please note that default dssp in Ubuntu 22.04 is not working properly.
.. code:: bash
wget https://github.com/cmbi/dssp/archive/refs/heads/master.zip && \
......@@ -75,6 +96,7 @@ Please note that default dssp in Ubuntu 22.04 is not working properly.
sudo rm -f master.zip
#HHSUITE installation
.. code:: bash
wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz && \
......@@ -88,16 +110,43 @@ Please note that default dssp in Ubuntu 22.04 is not working properly.
Check the location of hhsuite folder and add it to your path
In my case it was in /home/tekpinar/research/lcqb folder. Therefore, I added the following line
to my .profile file.
PATH="/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:$PATH"
Open .profile file with gedit:
Then
source ~/.profile
.. code:: bash
gedit ~/.profile
Now, add the following line to the end of the file.
.. code:: bash
PATH="/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:$PATH"
Of course, your path will not be /home/tekpinar/research/lcqb/ and you have to modify the path according to
your system. Save the file and exit. Then,
.. code:: bash
source ~/.profile
#
cd ESGEMME
#Download ESGEMME from http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME repository and go inside the ESGEMME folder.!
You can download the master version using command line as follows:
.. code:: bash
git clone http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
If you would like the development version:
.. code:: bash
git clone -b development http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
.. code:: bash
cd ESGEMME
......@@ -115,6 +164,7 @@ file according to your system.
cd ../
#Installing the required R packages
.. code:: bash
sudo Rscript -e 'install.packages("seqinr", repos="http://cran.us.r-project.org", dependencies=TRUE)'
......
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URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '1.3.0',
VERSION: '1.4.0',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: '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 ESGEMME Output &mdash; esgemme 1.3.0 documentation</title>
<title>Analyzing and Modifying the ESGEMME Output &mdash; esgemme 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Using ESGEMME via Docker &mdash; esgemme 1.3.0 documentation</title>
<title>Using ESGEMME via Docker &mdash; esgemme 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......@@ -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:v1.3.0
tekpinar/esgemme-docker:v1.4.0
</pre></div>
</div>
<p>You are in the container (your virtual operating system) now. You
......@@ -154,8 +154,7 @@ 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 -r input -f aliBLAT.fasta <span class="se">\</span>
--pdbfile blat-af2.pdb <span class="se">\</span>
--normweightmode sstjetormax
--pdbfile blat-af2.pdb
</pre></div>
</div>
</section>
......@@ -174,11 +173,12 @@ structural information. First, let’s do it without structural information:</p>
-m Stiffler_2015_BLAT_ECOLX.mut
</pre></div>
</div>
<p>You can include structural information in the following way:
.. code:: bash</p>
<blockquote>
<div><p>esgemme aliBLAT.fasta -r input -f aliBLAT.fasta –pdbfile blat-af2.pdb –normweightmode sstjetormax -m Stiffler_2015_BLAT_ECOLX.mut</p>
</div></blockquote>
<p>You can include structural information in the following way:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>esgemme aliBLAT.fasta -r input -f aliBLAT.fasta <span class="se">\</span>
--pdbfile blat-af2.pdb <span class="se">\</span>
-m Stiffler_2015_BLAT_ECOLX.mut
</pre></div>
</div>
<p>You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output
format is completely different from the entire mutational landscape scanning file.
Each line of this file is a mutation and its predicted effect separated by a space.
......
......@@ -3,7 +3,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Index &mdash; esgemme 1.3.0 documentation</title>
<title>Index &mdash; esgemme 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Welcome to esgemme’s documentation! &mdash; esgemme 1.3.0 documentation</title>
<title>Welcome to esgemme’s documentation! &mdash; esgemme 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Preparing Your Own Input &mdash; esgemme 1.3.0 documentation</title>
<title>Preparing Your Own Input &mdash; esgemme 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Installation &mdash; esgemme 1.3.0 documentation</title>
<title>Installation &mdash; esgemme 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......@@ -92,13 +92,24 @@ steps required to install it from the source.</p>
<ul>
<li><p>java</p></li>
<li><p>naccess: <a class="reference external" href="http://www.bioinf.manchester.ac.uk/naccess/">http://www.bioinf.manchester.ac.uk/naccess/</a></p></li>
<li><p>muscle: <a class="reference external" href="https://www.drive5.com/muscle/">https://www.drive5.com/muscle/</a></p></li>
</ul>
</li>
<li><p>seqinr R package: <a class="reference external" href="https://cran.r-project.org/web/packages/seqinr/index.html">https://cran.r-project.org/web/packages/seqinr/index.html</a></p></li>
<li><p>dssp for secondary structure prediction.</p></li>
</ul>
<p>These tools should be installed to be able to use ESGEMME.</p>
<p>After you installed JET2 define a parameter called JET2_PATH inside your .profile file.
You can open .profile as follows:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gedit ~/.profile
</pre></div>
</div>
<p>You should add a command like below to the end of that file, save and exit.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">JET2_PATH</span><span class="o">=</span>/home/tekpinar/JET2/
</pre></div>
</div>
<p>Please, do not forget to replace /home/tekpinar/JET2 with your own file path.</p>
<p>Then, source the saved .profile so that the environment variable will be taken into account:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">source</span> ~/.profile
</pre></div>
</div>
<p>JET2 is essential and it should be installed to be able to use ESGEMME.</p>
</section>
<section id="preparation-of-the-environment-and-installation-of-esgemme">
<h2>Preparation of the environment and installation of ESGEMME<a class="headerlink" href="#preparation-of-the-environment-and-installation-of-esgemme" title="Permalink to this heading"></a></h2>
......@@ -126,39 +137,67 @@ sudo apt-get clean <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
</pre></div>
</div>
<p>#Dssp installation
If you are using Ubuntu 20.04, you can install dssp by the following command
.. code:: bash</p>
<blockquote>
<div><p>sudo apt-get install dssp</p>
</div></blockquote>
<p>#Dssp installation</p>
<p>If you are using Ubuntu 20.04, you can install dssp by the following command</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo apt-get install dssp
</pre></div>
</div>
<p>Otherwise, you can install it from the source by the following commands.
Please note that default dssp in Ubuntu 22.04 is not working properly.
.. code:: bash</p>
<blockquote>
<div><p>wget <a class="reference external" href="https://github.com/cmbi/dssp/archive/refs/heads/master.zip">https://github.com/cmbi/dssp/archive/refs/heads/master.zip</a> &amp;&amp; unzip -o master.zip &amp;&amp; cd dssp-master/ &amp;&amp; ./autogen.sh &amp;&amp; ./configure &amp;&amp; make &amp;&amp; sudo make install &amp;&amp; sudo ln -s /usr/local/bin/mkdssp /usr/local/bin/dssp &amp;&amp; cd ../ &amp;&amp; sudo rm -rf dssp-master/ &amp;&amp; sudo rm -f master.zip</p>
</div></blockquote>
<p>#HHSUITE installation
.. code:: bash</p>
<blockquote>
<div><p>wget <a class="reference external" href="https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz">https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz</a> &amp;&amp; mkdir hhsuite &amp;&amp; mv hhsuite-3.3.0-AVX2-Linux.tar.gz hhsuite/ &amp;&amp; cd hhsuite &amp;&amp; tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz &amp;&amp; rm -f hhsuite-3.3.0-AVX2-Linux.tar.gz</p>
</div></blockquote>
Please note that default dssp in Ubuntu 22.04 is not working properly.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget https://github.com/cmbi/dssp/archive/refs/heads/master.zip <span class="o">&amp;&amp;</span> <span class="se">\</span>
unzip -o master.zip <span class="o">&amp;&amp;</span> <span class="nb">cd</span> dssp-master/ <span class="o">&amp;&amp;</span> <span class="se">\</span>
./autogen.sh <span class="o">&amp;&amp;</span> <span class="se">\</span>
./configure <span class="o">&amp;&amp;</span> <span class="se">\</span>
make <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo make install <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo ln -s /usr/local/bin/mkdssp /usr/local/bin/dssp <span class="o">&amp;&amp;</span> <span class="se">\</span>
<span class="nb">cd</span> ../ <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo rm -rf dssp-master/ <span class="o">&amp;&amp;</span> <span class="se">\</span>
sudo rm -f master.zip
</pre></div>
</div>
<p>#HHSUITE installation</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz <span class="o">&amp;&amp;</span> <span class="se">\</span>
mkdir hhsuite <span class="o">&amp;&amp;</span> <span class="se">\</span>
mv hhsuite-3.3.0-AVX2-Linux.tar.gz hhsuite/ <span class="o">&amp;&amp;</span> <span class="se">\</span>
<span class="nb">cd</span> hhsuite <span class="o">&amp;&amp;</span> <span class="se">\</span>
tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz <span class="o">&amp;&amp;</span> <span class="se">\</span>
rm -f hhsuite-3.3.0-AVX2-Linux.tar.gz
</pre></div>
</div>
<p>#Add it to your path permanently inside .bashrc or .profile or .bash_profile
Check the location of hhsuite folder and add it to your path
In my case it was in /home/tekpinar/research/lcqb folder. Therefore, I added the following line
to my .profile file.
PATH=”/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:$PATH”</p>
<p>Then
source ~/.profile</p>
Open .profile file with gedit:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gedit ~/.profile
</pre></div>
</div>
<p>Now, add the following line to the end of the file.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nv">PATH</span><span class="o">=</span><span class="s2">&quot;/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:</span><span class="nv">$PATH</span><span class="s2">&quot;</span>
</pre></div>
</div>
<p>Of course, your path will not be /home/tekpinar/research/lcqb/ and you have to modify the path according to
your system. Save the file and exit. Then,</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">source</span> ~/.profile
</pre></div>
</div>
<p>#</p>
<blockquote>
<div><p>cd ESGEMME</p>
</div></blockquote>
<p>#Download ESGEMME from <a class="reference external" href="http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME">http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME</a> repository and go inside the ESGEMME folder.!
.. code:: bash</p>
<blockquote>
<div><p>cd ESGEMME</p>
</div></blockquote>
You can download the master version using command line as follows:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git clone http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
</pre></div>
</div>
<p>If you would like the development version:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git clone -b development http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
</pre></div>
</div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> ESGEMME
</pre></div>
</div>
</section>
<section id="configuring-default-conf-file">
<h2>Configuring default.conf file<a class="headerlink" href="#configuring-default-conf-file" title="Permalink to this heading"></a></h2>
......@@ -170,11 +209,10 @@ file according to your system.</p>
<span class="nb">cd</span> ../
</pre></div>
</div>
<p>#Installing the required R packages
.. code:: bash</p>
<blockquote>
<div><p>sudo Rscript -e ‘install.packages(“seqinr”, repos=”<a class="reference external" href="http://cran.us.r-project.org">http://cran.us.r-project.org</a>”, dependencies=TRUE)’</p>
</div></blockquote>
<p>#Installing the required R packages</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo Rscript -e <span class="s1">&#39;install.packages(&quot;seqinr&quot;, repos=&quot;http://cran.us.r-project.org&quot;, dependencies=TRUE)&#39;</span>
</pre></div>
</div>
<p>#Installing secondary programs such as ev_couplings to obtain MSA files.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget https://github.com/debbiemarkslab/plmc/archive/refs/heads/master.zip <span class="o">&amp;&amp;</span> <span class="se">\</span>
unzip -o master.zip <span class="o">&amp;&amp;</span> <span class="se">\</span>
......
......@@ -3,7 +3,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Search &mdash; esgemme 1.3.0 documentation</title>
<title>Search &mdash; esgemme 1.4.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
......
......@@ -66,8 +66,8 @@
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......
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......@@ -140,13 +140,13 @@
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......@@ -161,7 +161,7 @@
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"sphinxpackagefootnote.sty" 1657784170 15217 dd26fe418b6fb1b26b18f042a7f43d40 ""
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[]\T1/qtm/m/n/10 Con-grat-u-la-tions! Now, you have all the in-put files re-qui
red for ES-GEMME: I. An in-put MSA:
[]
......@@ -814,18 +814,12 @@ red for ES-GEMME: I. An in-put MSA:
[8]
Chapter 4.
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in-stall && sudo ln -s
[]
[10] [11] [12
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Chapter 5.
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......@@ -61,8 +61,8 @@
\title{esgemme}
\date{Jun 22, 2023}
\release{1.3.0}
\date{Jul 31, 2023}
\release{1.4.0}
\author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}}
\renewcommand{\releasename}{Release}
......@@ -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:v1.3.0
tekpinar/esgemme\PYGZhy{}docker:v1.4.0
\end{sphinxVerbatim}
\sphinxAtStartPar
......@@ -195,8 +195,7 @@ evolutionary information:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
esgemme aliBLAT.fasta \PYGZhy{}r input \PYGZhy{}f aliBLAT.fasta \PYG{l+s+se}{\PYGZbs{}}
\PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb \PYG{l+s+se}{\PYGZbs{}}
\PYGZhy{}\PYGZhy{}normweightmode sstjetormax
\PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb
\end{sphinxVerbatim}
......@@ -223,12 +222,12 @@ esgemme aliBLAT.fasta \PYGZhy{}r input \PYGZhy{}f aliBLAT.fasta \PYG{l+s+se}{\PY
\sphinxAtStartPar
You can include structural information in the following way:
.. code:: bash
\begin{quote}
\sphinxAtStartPar
esgemme aliBLAT.fasta \sphinxhyphen{}r input \sphinxhyphen{}f aliBLAT.fasta \textendash{}pdbfile blat\sphinxhyphen{}af2.pdb \textendash{}normweightmode sstjetormax \sphinxhyphen{}m Stiffler\_2015\_BLAT\_ECOLX.mut
\end{quote}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
esgemme aliBLAT.fasta \PYGZhy{}r input \PYGZhy{}f aliBLAT.fasta \PYG{l+s+se}{\PYGZbs{}}
\PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb \PYG{l+s+se}{\PYGZbs{}}
\PYGZhy{}m Stiffler\PYGZus{}2015\PYGZus{}BLAT\PYGZus{}ECOLX.mut
\end{sphinxVerbatim}
\sphinxAtStartPar
You will have BLAT\_normPred\_evolCombi.txt file in your folder. However, the output
......@@ -491,24 +490,37 @@ java
\sphinxAtStartPar
naccess: \sphinxurl{http://www.bioinf.manchester.ac.uk/naccess/}
\item {}
\sphinxAtStartPar
muscle: \sphinxurl{https://www.drive5.com/muscle/}
\end{itemize}
\end{itemize}
\item {}
\sphinxAtStartPar
seqinr R package: \sphinxurl{https://cran.r-project.org/web/packages/seqinr/index.html}
After you installed JET2 define a parameter called JET2\_PATH inside your .profile file.
You can open .profile as follows:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
gedit \PYGZti{}/.profile
\end{sphinxVerbatim}
\item {}
\sphinxAtStartPar
dssp for secondary structure prediction.
You should add a command like below to the end of that file, save and exit.
\end{itemize}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{n+nb}{export} \PYG{n+nv}{JET2\PYGZus{}PATH}\PYG{o}{=}/home/tekpinar/JET2/
\end{sphinxVerbatim}
\sphinxAtStartPar
Please, do not forget to replace /home/tekpinar/JET2 with your own file path.
\sphinxAtStartPar
Then, source the saved .profile so that the environment variable will be taken into account:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{n+nb}{source} \PYGZti{}/.profile
\end{sphinxVerbatim}
\sphinxAtStartPar
These tools should be installed to be able to use ESGEMME.
JET2 is essential and it should be installed to be able to use ESGEMME.
\section{Preparation of the environment and installation of ESGEMME}
......@@ -544,43 +556,68 @@ sudo rm \PYGZhy{}rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
\sphinxAtStartPar
\#Dssp installation
If you are using Ubuntu 20.04, you can install dssp by the following command
.. code:: bash
\begin{quote}
\sphinxAtStartPar
sudo apt\sphinxhyphen{}get install dssp
\end{quote}
If you are using Ubuntu 20.04, you can install dssp by the following command
\begin{sphinxVerbatim}[commandchars=\\\{\}]
sudo apt\PYGZhy{}get install dssp
\end{sphinxVerbatim}
\sphinxAtStartPar
Otherwise, you can install it from the source by the following commands.
Please note that default dssp in Ubuntu 22.04 is not working properly.
.. code:: bash
\begin{quote}
\sphinxAtStartPar
wget \sphinxurl{https://github.com/cmbi/dssp/archive/refs/heads/master.zip} \&\& unzip \sphinxhyphen{}o master.zip \&\& cd dssp\sphinxhyphen{}master/ \&\& ./autogen.sh \&\& ./configure \&\& make \&\& sudo make install \&\& sudo ln \sphinxhyphen{}s /usr/local/bin/mkdssp /usr/local/bin/dssp \&\& cd ../ \&\& sudo rm \sphinxhyphen{}rf dssp\sphinxhyphen{}master/ \&\& sudo rm \sphinxhyphen{}f master.zip
\end{quote}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
wget https://github.com/cmbi/dssp/archive/refs/heads/master.zip \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{l+s+se}{\PYGZbs{}}
unzip \PYGZhy{}o master.zip \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{n+nb}{cd} dssp\PYGZhy{}master/ \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{l+s+se}{\PYGZbs{}}
./autogen.sh \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{l+s+se}{\PYGZbs{}}
./configure \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{l+s+se}{\PYGZbs{}}
make \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{l+s+se}{\PYGZbs{}}
sudo make install \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{l+s+se}{\PYGZbs{}}
sudo ln \PYGZhy{}s /usr/local/bin/mkdssp /usr/local/bin/dssp \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{l+s+se}{\PYGZbs{}}
\PYG{n+nb}{cd} ../ \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{l+s+se}{\PYGZbs{}}
sudo rm \PYGZhy{}rf dssp\PYGZhy{}master/ \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{l+s+se}{\PYGZbs{}}
sudo rm \PYGZhy{}f master.zip
\end{sphinxVerbatim}
\sphinxAtStartPar
\#HHSUITE installation
.. code:: bash
\begin{quote}
\sphinxAtStartPar
wget \sphinxurl{https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz} \&\& mkdir hhsuite \&\& mv hhsuite\sphinxhyphen{}3.3.0\sphinxhyphen{}AVX2\sphinxhyphen{}Linux.tar.gz hhsuite/ \&\& cd hhsuite \&\& tar xvfz hhsuite\sphinxhyphen{}3.3.0\sphinxhyphen{}AVX2\sphinxhyphen{}Linux.tar.gz \&\& rm \sphinxhyphen{}f hhsuite\sphinxhyphen{}3.3.0\sphinxhyphen{}AVX2\sphinxhyphen{}Linux.tar.gz
\end{quote}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
wget https://github.com/soedinglab/hh\PYGZhy{}suite/releases/download/v3.3.0/hhsuite\PYGZhy{}3.3.0\PYGZhy{}AVX2\PYGZhy{}Linux.tar.gz \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{l+s+se}{\PYGZbs{}}
mkdir hhsuite \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{l+s+se}{\PYGZbs{}}
mv hhsuite\PYGZhy{}3.3.0\PYGZhy{}AVX2\PYGZhy{}Linux.tar.gz hhsuite/ \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{l+s+se}{\PYGZbs{}}
\PYG{n+nb}{cd} hhsuite \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{l+s+se}{\PYGZbs{}}
tar xvfz hhsuite\PYGZhy{}3.3.0\PYGZhy{}AVX2\PYGZhy{}Linux.tar.gz \PYG{o}{\PYGZam{}\PYGZam{}} \PYG{l+s+se}{\PYGZbs{}}
rm \PYGZhy{}f hhsuite\PYGZhy{}3.3.0\PYGZhy{}AVX2\PYGZhy{}Linux.tar.gz
\end{sphinxVerbatim}
\sphinxAtStartPar
\#Add it to your path permanently inside .bashrc or .profile or .bash\_profile
Check the location of hhsuite folder and add it to your path
In my case it was in /home/tekpinar/research/lcqb folder. Therefore, I added the following line
to my .profile file.
PATH=”/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:\$PATH”
Open .profile file with gedit:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
gedit \PYGZti{}/.profile
\end{sphinxVerbatim}
\sphinxAtStartPar
Then
source \textasciitilde{}/.profile
Now, add the following line to the end of the file.
\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{n+nv}{PATH}\PYG{o}{=}\PYG{l+s+s2}{\PYGZdq{}}\PYG{l+s+s2}{/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:}\PYG{n+nv}{\PYGZdl{}PATH}\PYG{l+s+s2}{\PYGZdq{}}
\end{sphinxVerbatim}
\sphinxAtStartPar
Of course, your path will not be /home/tekpinar/research/lcqb/ and you have to modify the path according to
your system. Save the file and exit. Then,
\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{n+nb}{source} \PYGZti{}/.profile
\end{sphinxVerbatim}
\sphinxAtStartPar
\#
......@@ -592,12 +629,22 @@ cd ESGEMME
\sphinxAtStartPar
\#Download ESGEMME from \sphinxurl{http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME} repository and go inside the ESGEMME folder.!
.. code:: bash
\begin{quote}
You can download the master version using command line as follows:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
git clone http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
\end{sphinxVerbatim}
\sphinxAtStartPar
cd ESGEMME
\end{quote}
If you would like the development version:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
git clone \PYGZhy{}b development http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
\end{sphinxVerbatim}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{n+nb}{cd} ESGEMME
\end{sphinxVerbatim}
\section{Configuring default.conf file}
......@@ -615,12 +662,10 @@ pip3 install \PYGZhy{}e . \PYG{o}{\PYGZam{}\PYGZam{}}\PYG{l+s+se}{\PYGZbs{}}
\sphinxAtStartPar
\#Installing the required R packages
.. code:: bash
\begin{quote}
\sphinxAtStartPar
sudo Rscript \sphinxhyphen{}e ‘install.packages(“seqinr”, repos=”\sphinxurl{http://cran.us.r-project.org}”, dependencies=TRUE)’
\end{quote}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
sudo Rscript \PYGZhy{}e \PYG{l+s+s1}{\PYGZsq{}install.packages(\PYGZdq{}seqinr\PYGZdq{}, repos=\PYGZdq{}http://cran.us.r\PYGZhy{}project.org\PYGZdq{}, dependencies=TRUE)\PYGZsq{}}
\end{sphinxVerbatim}
\sphinxAtStartPar
\#Installing secondary programs such as ev\_couplings to obtain MSA files.
......
......@@ -16,5 +16,5 @@
\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 ESGEMME}{9}{section.4.2}%
\contentsline {section}{\numberline {4.3}Configuring default.conf file}{10}{section.4.3}%
\contentsline {section}{\numberline {4.3}Configuring default.conf file}{11}{section.4.3}%
\contentsline {chapter}{\numberline {5}Indices and tables}{13}{chapter.5}%
......@@ -23,7 +23,7 @@ copyright = '2023, Mustafa Tekpinar'
author = 'Mustafa Tekpinar'
# The full version, including alpha/beta/rc tags
release = '1.3.0'
release = '1.4.0'
# -- General configuration ---------------------------------------------------
......
......@@ -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=$PWD,target=/home/tekpinar/research/myexample \
tekpinar/esgemme-docker:v1.3.0
tekpinar/esgemme-docker:v1.4.0
You are in the container (your virtual operating system) now. You
created a folder called myexample in your container with the previous
......@@ -94,8 +94,7 @@ evolutionary information:
.. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
--normweightmode sstjetormax
--pdbfile blat-af2.pdb
Predicting the effect of a subset of single point mutations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
......@@ -117,11 +116,11 @@ structural information. First, let's do it without structural information:
-m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way:
.. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
--normweightmode sstjetormax \
-m Stiffler_2015_BLAT_ECOLX.mut
You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output
......
......@@ -72,13 +72,16 @@ Prepare your environment and install the required packages:
#Dssp installation
If you are using Ubuntu 20.04, you can install dssp by the following command
.. code:: bash
sudo apt-get install dssp
Otherwise, you can install it from the source by the following commands.
Please note that default dssp in Ubuntu 22.04 is not working properly.
.. code:: bash
wget https://github.com/cmbi/dssp/archive/refs/heads/master.zip && \
......@@ -93,6 +96,7 @@ Please note that default dssp in Ubuntu 22.04 is not working properly.
sudo rm -f master.zip
#HHSUITE installation
.. code:: bash
wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz && \
......@@ -117,6 +121,7 @@ Now, add the following line to the end of the file.
.. code:: bash
PATH="/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:$PATH"
Of course, your path will not be /home/tekpinar/research/lcqb/ and you have to modify the path according to
your system. Save the file and exit. Then,
......@@ -132,6 +137,7 @@ your system. Save the file and exit. Then,
You can download the master version using command line as follows:
.. code:: bash
git clone http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
If you would like the development version:
......
......@@ -972,7 +972,7 @@ def parse_command_line():
parser.add_argument('--normweightmode', dest='normweightmode', type=str, \
help="It can be one of these: 'tjet', 'cv', 'pc',"+\
"max, tjetormax or sstjetormaxtwocomponent. Default is 'tjet'.",
required=False, default="sstjetormaxtwocomponent")
required=False, default="tjet")
parser.add_argument('--verbose', dest='verbose', type=bool, \
help="This argument controls amount of the output. Default is 'False'."+\
......@@ -1441,6 +1441,14 @@ def main():
args = parse_command_line()
# If a structure file is provided, utilize structural information.
if(args.pdbfile==None):
args.normweightmode='tjet'
print("Using '{}' as normalization weight.".format(args.normweightmode))
else:
args.normweightmode='sstjetormaxtwocomponent'
print("Using '{}' as normalization weight.".format(args.normweightmode))
doit(args.input, args.mutations, args.retrievingMethod, args.blastFile,\
args.fastaFile, args.nIter,args.NSeqs, args.jetfile, args.pdbfile,\
args.normweightmode, args.alphabet, args.verbose, args.offset, \
......
......@@ -29,7 +29,7 @@ then
echo "Using blat-af2.pdb for the structural feature calculations!"
echo "Entire mutational map of the protein will be calculated!"
esgemme ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
--pdbfile ../data/blat-af2.pdb --normweightmode max
--pdbfile ../data/blat-af2.pdb
elif [ "$1" == "withpdb-withmutfile" ]
then
......@@ -38,28 +38,7 @@ then
echo "Using blat-af2.pdb for the structural feature calculations!"
echo "Only effects of mutations specified in the Stiffler_2015_BLAT_ECOLX.mut file will be calculated!"
esgemme ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
--pdbfile ../data/blat-af2.pdb --normweightmode max \
-m ../data/Stiffler_2015_BLAT_ECOLX.mut
elif [ "$1" == "sstjetormax" ]
then
#Please note that CV isa structural feature and it can not be calculated if you don't specify a pdb file.
echo "Using blat-af2.pdb for the secondary structure based calculations!"
echo "Only effects of mutations specified in the Stiffler_2015_BLAT_ECOLX.mut file will be calculated!"
esgemme ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
--pdbfile ../data/blat-af2.pdb --normweightmode sstjetormax \
-m ../data/Stiffler_2015_BLAT_ECOLX.mut
demust compare -i ../data/BLAT_ECOLX_Stiffler_2015_experimental.dat --itype singleline -j BLAT_normPred_evolCombi.txt --jtype singleline
elif [ "$1" == "tjetormax" ]
then
#Please note that CV isa structural feature and it can not be calculated if you don't specify a pdb file.
echo "Using blat-af2.pdb for the secondary structure based calculations!"
echo "Only effects of mutations specified in the Stiffler_2015_BLAT_ECOLX.mut file will be calculated!"
esgemme ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
--pdbfile ../data/blat-af2.pdb --normweightmode tjetormax \
-m ../data/Stiffler_2015_BLAT_ECOLX.mut
--pdbfile ../data/blat-af2.pdb -m ../data/Stiffler_2015_BLAT_ECOLX.mut
demust compare -i ../data/BLAT_ECOLX_Stiffler_2015_experimental.dat --itype singleline -j BLAT_normPred_evolCombi.txt --jtype singleline
else
......
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