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PRESCOTT
Commit 468bf9aa by Mustafa Tekpinar
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Changed program name from ESGEMME to PRESCOTT.

parent fdc001bc
Showing with 187 additions and 187 deletions
Dockerfile
FROM ubuntu:22.04
LABEL maintainer="Mustafa Tekpinar <tekpinar@buffalo.edu>"
LABEL description="ESGEMME: Evolutionary and Structural Global Epistatic Model for predicting Mutational Effects."
LABEL description="PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs"
ENV DEBIAN_FRONTEND=noninteractive
WORKDIR /home/tekpinar/research/lcqb
ENV JET2_PATH=/usr/local/JET2
ENV ESGEMME_PATH=/home/tekpinar/research/lcqb/ESGEMME
ENV PRESCOTT_PATH=/home/tekpinar/research/lcqb/PRESCOTT
COPY ./JET2/ /usr/local/JET2
COPY ./naccess2.1.1 /usr/local/naccess2.1.1
COPY ./ESGEMME/esgemme/esgemme.py ./ESGEMME/esgemme/esgemme.py
COPY ./ESGEMME/esgemme/alphabets ./ESGEMME/esgemme/alphabets
COPY ./ESGEMME/esgemme/__init__.py ./ESGEMME/esgemme/__init__.py
COPY ./ESGEMME/setup.py ./ESGEMME/setup.py
COPY ./ESGEMME/requirements.txt ./ESGEMME/requirements.txt
COPY ./ESGEMME/README.md ./ESGEMME/README.md
COPY ./ESGEMME/esgemme/pred.R ./ESGEMME/esgemme/pred.R
COPY ./ESGEMME/esgemme/computePred.R ./ESGEMME/esgemme/computePred.R
COPY ./ESGEMME/esgemme/default.conf ./ESGEMME/esgemme/default.conf
COPY ./ESGEMME/data/ ./ESGEMME/data/
COPY ./ESGEMME/examples/ ./ESGEMME/examples/
COPY ./PRESCOTT/esgemme/esgemme.py ./PRESCOTT/esgemme/esgemme.py
COPY ./PRESCOTT/esgemme/alphabets ./PRESCOTT/esgemme/alphabets
COPY ./PRESCOTT/esgemme/__init__.py ./PRESCOTT/esgemme/__init__.py
COPY ./PRESCOTT/setup.py ./PRESCOTT/setup.py
COPY ./PRESCOTT/requirements.txt ./PRESCOTT/requirements.txt
COPY ./PRESCOTT/README.md ./PRESCOTT/README.md
COPY ./PRESCOTT/esgemme/pred.R ./PRESCOTT/esgemme/pred.R
COPY ./PRESCOTT/esgemme/computePred.R ./PRESCOTT/esgemme/computePred.R
COPY ./PRESCOTT/esgemme/default.conf ./PRESCOTT/esgemme/default.conf
COPY ./PRESCOTT/data/ ./PRESCOTT/data/
COPY ./PRESCOTT/examples/ ./PRESCOTT/examples/
COPY ./demust/ ./demust/
###################################################################
......@@ -75,9 +75,9 @@ ENV PATH="/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/
RUN rm -f hhsuite-3.3.0-AVX2-Linux.tar.gz
WORKDIR /home/tekpinar/research/lcqb
RUN sed -i s#/home/tekpinar/research/lcqb/JET2/matrix#/usr/local/JET2/matrix#g ./ESGEMME/esgemme/default.conf
RUN sed -i s#/home/tekpinar/research/lcqb/naccess2.1.1/naccess#/usr/local/naccess2.1.1/naccess#g ./ESGEMME/esgemme/default.conf
RUN pip3 install ./ESGEMME/
RUN sed -i s#/home/tekpinar/research/lcqb/JET2/matrix#/usr/local/JET2/matrix#g ./PRESCOTT/esgemme/default.conf
RUN sed -i s#/home/tekpinar/research/lcqb/naccess2.1.1/naccess#/usr/local/naccess2.1.1/naccess#g ./PRESCOTT/esgemme/default.conf
RUN pip3 install ./PRESCOTT/
RUN pip3 install -e ./demust/
RUN Rscript -e 'install.packages("seqinr", repos="http://cran.us.r-project.org", dependencies=TRUE)'
......
README.md
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
![image info](./images/esgemme-image.png)
# ESGEMME: Evolutionary and Structural Global Epistatic Model for Mutational Effects
# PRESCOTT: Evolutionary and Structural Global Epistatic Model for Mutational Effects
## Introduction
ESGEMME is a program predicting mutational effects of a protein based on evolutionary and structural information.
PRESCOTT is a program predicting mutational effects of a protein based on evolutionary and structural information.
It can calculate effects of single point mutations and multiple point mutations.
We recommend using ESGEMME via our web site or our docker image.
We recommend using PRESCOTT via our web site or our docker image.
## Input Data Requirements
ESGEMME requires two files:
PRESCOTT 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.
......@@ -22,7 +22,7 @@ ESGEMME requires two files:
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 ESGEMME. You can remove the gaps with pragrams that have a GUI, such as ugene (http://ugene.net/) or jalview (https://www.jalview.org/).
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 example input files for BLAT protein in data/ folder of this repository.
......@@ -32,12 +32,12 @@ Let's assume that our input MSA is inputAli.fasta and input.pdb is our structure
Run the program by issuing the following command in a bash terminal:
```bash
python $ESGEMME_PATH/esgemme.py inputAli.fasta --pdbfile input.pdb
python $PRESCOTT_PATH/esgemme.py inputAli.fasta --pdbfile input.pdb
```
A quick help can be accessed by typing
```bash
python $ESGEMME_PATH/esgemme.py --help
python $PRESCOTT_PATH/esgemme.py --help
```
By default, GEMME will predict the effect of all possible single mutations at all positions in the
......@@ -56,7 +56,7 @@ JET2 configuration file is: default.conf.
JET2 output file is: myProt_jet.res.
## Installation
ESGEMME is implemented in Python 3 and R. It has been tested only on Linux. Since ESGEMME 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):
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):
# Cite
......
docs/_build/html/_sources/analysis.rst.txt
Analyzing and Modifying the ESGEMME Output
Analyzing and Modifying the PRESCOTT Output
==========================================
Raw ESGEMME Scores and Their Interpretation
Raw PRESCOTT Scores and Their Interpretation
-------------------------------------------
There is not a hardcoded limit for raw ESGEMME scores. However, the values
There is not a hardcoded limit for raw PRESCOTT scores. However, the values
range between [-12, 2] generally. The lower values mean the mutations is impactful,
while values close to 0 means the mutation does not have any significant impact.
......@@ -13,7 +13,7 @@ it is not always the case.
Entire Single Point Mutation Landscape Calculations
---------------------------------------------------
By default, ESGEMME will only output the combined (independent
By default, PRESCOTT will only output the combined (independent
and epistatic) scores*:
There are three output files:
......
docs/_build/html/_sources/docker.rst.txt
Using ESGEMME via Docker
Using PRESCOTT via Docker
========================
Requirements
......@@ -23,19 +23,19 @@ folder:
Getting the example input data
------------------------------
Let’s download the sample data provided in the ESGEMME repository for
Let’s download the sample data provided in the PRESCOTT repository for
this exercise. First, we will download the multiple sequence alignment
file in fasta format:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta
wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta
If you don’t have wget, you can try the same command with curl:
.. code:: bash
curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta >aliBLAT.fasta
curl http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta >aliBLAT.fasta
Please verify that the aliBLAT.fasta file is in the folder.
......@@ -43,7 +43,7 @@ Now, we will download the PDB (Protein Databank) file for BLAT:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/blat-af2.pdb
wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/blat-af2.pdb
Single point mutation calculations
----------------------------------
......@@ -100,11 +100,11 @@ Predicting the effect of a subset of single point mutations
If you are interested in only a bunch of single point mutations,
you have to prepare a mut file. The format is a simple text file and
each line contains a single point mutation such as D26A....
Fortunately, we have an example mut in data folder of ESGEMME repository.
Fortunately, we have an example mut in data folder of PRESCOTT repository.
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/master/data/Stiffler_2015_BLAT_ECOLX.mut
wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/master/data/Stiffler_2015_BLAT_ECOLX.mut
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:
......@@ -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. ESGEMME can
Sometimes, we need to see effects of double or triple mutations. PRESCOTT can
perform calculations if you provide a mut file. In this case, the mut file must
have the following format:
......
docs/_build/html/_sources/input-preparation.rst.txt
......@@ -36,7 +36,7 @@ structure is to use Colabfold. Let's do this step by step:
7. Unfortunately, a3m file is not in fasta format and it contains gap columns.
We have to clean those gaps. We can do that with a GUI program like Ugene
or Jalview. However, it is a labor intensive procedure. Here, I will use a
small tool that I developed and added to the ESGEMME docker image that I created.
small tool that I developed and added to the PRESCOTT docker image that I created.
8. Start the docker image with the following command:
......@@ -75,7 +75,7 @@ a3m and fasta files are too long. We have to shorten them. We can do that with
# Recheck this command if you can remove extra >
Congratulations! Now, you have all the input files required for ESGEMME:
Congratulations! Now, you have all the input files required for PRESCOTT:
I. An input MSA: AKE_nogaps_short_names.fasta
II. An input PDB: myprotein.pdb
......
docs/_build/html/_sources/installation.rst.txt
Installation
------------
ESGEMME is implemented in Python 3 and R. It has been tested only on
Linux. Since ESGEMME has many dependencies, we recommend using our web
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, here comes the
steps required to install it from the source.
Installing the dependencies:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ESGEMME has the following external dependencies:
PRESCOTT has the following external dependencies:
* Joint Evolutionary Trees: http://www.lcqb.upmc.fr/JET2/ and its dependencies:
......@@ -38,9 +38,9 @@ Then, source the saved .profile so that the environment variable will be taken i
source ~/.profile
JET2 is essential and it should be installed to be able to use ESGEMME.
JET2 is essential and it should be installed to be able to use PRESCOTT.
Preparation of the environment and installation of ESGEMME
Preparation of the environment and installation of PRESCOTT
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step by step installation on Ubuntu 22.04
......@@ -131,30 +131,30 @@ your system. Save the file and exit. Then,
#
cd ESGEMME
cd PRESCOTT
#Download ESGEMME from http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME repository and go inside the ESGEMME folder.!
#Download PRESCOTT from http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT repository and go inside the PRESCOTT folder.!
You can download the master version using command line as follows:
.. code:: bash
git clone http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
git clone http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT.git
If you would like the development version:
.. code:: bash
git clone -b development http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
git clone -b development http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT.git
.. code:: bash
cd ESGEMME
cd PRESCOTT
Configuring default.conf file
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Inside ESGEMME/esgemme folder, there is an important file called default.conf.
This file contains essential parameters of ESGEMME, such as paths of
Inside PRESCOTT/esgemme folder, there is an important file called default.conf.
This file contains essential parameters of PRESCOTT, such as paths of
external parts, default internal parameters. etc. You have to correct the Software section of this
file according to your system.
......
docs/_build/html/analysis.html
......@@ -4,7 +4,7 @@
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......@@ -44,9 +44,9 @@
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<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="docker.html">Using ESGEMME via Docker</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Analyzing and Modifying the ESGEMME Output</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#raw-esgemme-scores-and-their-interpretation">Raw ESGEMME Scores and Their Interpretation</a></li>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using PRESCOTT via Docker</a></li>
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<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 +69,7 @@
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......@@ -80,10 +80,10 @@
<div itemprop="articleBody">
<section id="analyzing-and-modifying-the-esgemme-output">
<h1>Analyzing and Modifying the ESGEMME Output<a class="headerlink" href="#analyzing-and-modifying-the-esgemme-output" title="Permalink to this heading"></a></h1>
<h1>Analyzing and Modifying the PRESCOTT Output<a class="headerlink" href="#analyzing-and-modifying-the-esgemme-output" title="Permalink to this heading"></a></h1>
<section id="raw-esgemme-scores-and-their-interpretation">
<h2>Raw ESGEMME Scores and Their Interpretation<a class="headerlink" href="#raw-esgemme-scores-and-their-interpretation" title="Permalink to this heading"></a></h2>
<p>There is not a hardcoded limit for raw ESGEMME scores. However, the values
<h2>Raw PRESCOTT Scores and Their Interpretation<a class="headerlink" href="#raw-esgemme-scores-and-their-interpretation" title="Permalink to this heading"></a></h2>
<p>There is not a hardcoded limit for raw PRESCOTT scores. However, the values
range between [-12, 2] generally. The lower values mean the mutations is impactful,
while values close to 0 means the mutation does not have any significant impact.</p>
<p>We should note that most of the ‘impactful’ mutations are deleterious but
......@@ -91,7 +91,7 @@ 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, ESGEMME will only output the combined (independent
<p>By default, PRESCOTT will only output the combined (independent
and epistatic) scores*:</p>
<p>There are three output files:</p>
<ol class="arabic">
......@@ -143,7 +143,7 @@ D286F -0.23</p>
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......@@ -4,7 +4,7 @@
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......@@ -44,7 +44,7 @@
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<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 ESGEMME via Docker</a><ul>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Using PRESCOTT 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>
......@@ -56,7 +56,7 @@
<li class="toctree-l2"><a class="reference internal" href="#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 ESGEMME Output</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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......@@ -75,7 +75,7 @@
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<section id="using-esgemme-via-docker">
<h1>Using ESGEMME via Docker<a class="headerlink" href="#using-esgemme-via-docker" title="Permalink to this heading"></a></h1>
<h1>Using PRESCOTT via Docker<a class="headerlink" href="#using-esgemme-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
......@@ -103,19 +103,19 @@ folder:</p>
</section>
<section id="getting-the-example-input-data">
<h2>Getting the example input data<a class="headerlink" href="#getting-the-example-input-data" title="Permalink to this heading"></a></h2>
<p>Let’s download the sample data provided in the ESGEMME repository for
<p>Let’s download the sample data provided in the PRESCOTT repository for
this exercise. First, we will download the multiple sequence alignment
file in fasta format:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta
</pre></div>
</div>
<p>If you don’t have wget, you can try the same command with curl:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta &gt;aliBLAT.fasta
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>curl http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta &gt;aliBLAT.fasta
</pre></div>
</div>
<p>Please verify that the aliBLAT.fasta file is in the folder.</p>
<p>Now, we will download the PDB (Protein Databank) file for BLAT:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/blat-af2.pdb
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/blat-af2.pdb
</pre></div>
</div>
</section>
......@@ -162,8 +162,8 @@ evolutionary information:</p>
<p>If you are interested in only a bunch of single point mutations,
you have to prepare a mut file. The format is a simple text file and
each line contains a single point mutation such as D26A….
Fortunately, we have an example mut in data folder of ESGEMME repository.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/master/data/Stiffler_2015_BLAT_ECOLX.mut
Fortunately, we have an example mut in data folder of PRESCOTT repository.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/master/data/Stiffler_2015_BLAT_ECOLX.mut
</pre></div>
</div>
<p>Similar to the previous step, there are two possible ways to do the calculations: with or without
......@@ -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. ESGEMME can
<p>Sometimes, we need to see effects of double or triple mutations. PRESCOTT 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
......@@ -207,7 +207,7 @@ mutation and its predicted effect, separated by a space.</p>
</div>
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......@@ -19,7 +19,7 @@
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<li class="toctree-l1"><a class="reference internal" href="docker.html">Using PRESCOTT via Docker</a></li>
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......@@ -78,7 +78,7 @@
<div class="toctree-wrapper compound">
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<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a><ul>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using PRESCOTT via Docker</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="docker.html#single-point-mutation-calculations">Single point mutation calculations</a></li>
......@@ -86,8 +86,8 @@
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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-l2"><a class="reference internal" href="analysis.html#raw-esgemme-scores-and-their-interpretation">Raw PRESCOTT Scores and Their Interpretation</a></li>
<li class="toctree-l2"><a class="reference internal" href="analysis.html#entire-single-point-mutation-landscape-calculations">Entire Single Point Mutation Landscape Calculations</a></li>
<li class="toctree-l2"><a class="reference internal" href="analysis.html#selected-single-point-or-multiple-point-mutation-calculations">Selected Single Point or Multiple Point Mutation Calculations</a></li>
</ul>
......@@ -98,7 +98,7 @@
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<li class="toctree-l2"><a class="reference internal" href="installation.html#preparation-of-the-environment-and-installation-of-esgemme">Preparation of the environment and installation of ESGEMME</a></li>
<li class="toctree-l2"><a class="reference internal" href="installation.html#preparation-of-the-environment-and-installation-of-esgemme">Preparation of the environment and installation of PRESCOTT</a></li>
<li class="toctree-l2"><a class="reference internal" href="installation.html#configuring-default-conf-file">Configuring default.conf file</a></li>
</ul>
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......@@ -118,7 +118,7 @@
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......@@ -20,7 +20,7 @@
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Installation" href="installation.html" />
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<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 ESGEMME via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESGEMME Output</a></li>
<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="analysis.html">Analyzing and Modifying the PRESCOTT Output</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Preparing Your Own Input</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#preparing-your-input-msa-and-pdb-with-colabfold">Preparing Your Input MSA and PDB with Colabfold</a></li>
</ul>
......@@ -106,7 +106,7 @@ terminal.</p></li>
<li><p>Unfortunately, a3m file is not in fasta format and it contains gap columns.
We have to clean those gaps. We can do that with a GUI program like Ugene
or Jalview. However, it is a labor intensive procedure. Here, I will use a
small tool that I developed and added to the ESGEMME docker image that I created.</p></li>
small tool that I developed and added to the PRESCOTT docker image that I created.</p></li>
<li><p>Start the docker image with the following command:</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
......@@ -139,7 +139,7 @@ a3m and fasta files are too long. We have to shorten them. We can do that with</
</pre></div>
</div>
</div></blockquote>
<p>Congratulations! Now, you have all the input files required for ESGEMME:
<p>Congratulations! Now, you have all the input files required for PRESCOTT:
I. An input MSA: AKE_nogaps_short_names.fasta
II. An input PDB: myprotein.pdb</p>
</section>
......@@ -149,7 +149,7 @@ II. An input PDB: myprotein.pdb</p>
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......@@ -43,12 +43,12 @@
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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="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>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#installing-the-dependencies">Installing the dependencies:</a></li>
<li class="toctree-l2"><a class="reference internal" href="#preparation-of-the-environment-and-installation-of-esgemme">Preparation of the environment and installation of ESGEMME</a></li>
<li class="toctree-l2"><a class="reference internal" href="#preparation-of-the-environment-and-installation-of-esgemme">Preparation of the environment and installation of PRESCOTT</a></li>
<li class="toctree-l2"><a class="reference internal" href="#configuring-default-conf-file">Configuring default.conf file</a></li>
</ul>
</li>
......@@ -80,13 +80,13 @@
<section id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this heading"></a></h1>
<p>ESGEMME is implemented in Python 3 and R. It has been tested only on
Linux. Since ESGEMME has many dependencies, we recommend using our web
<p>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, here comes the
steps required to install it from the source.</p>
<section id="installing-the-dependencies">
<h2>Installing the dependencies:<a class="headerlink" href="#installing-the-dependencies" title="Permalink to this heading"></a></h2>
<p>ESGEMME has the following external dependencies:</p>
<p>PRESCOTT has the following external dependencies:</p>
<ul class="simple">
<li><p>Joint Evolutionary Trees: <a class="reference external" href="http://www.lcqb.upmc.fr/JET2/">http://www.lcqb.upmc.fr/JET2/</a> and its dependencies:</p>
<ul>
......@@ -109,10 +109,10 @@ You can open .profile as follows:</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>
<p>JET2 is essential and it should be installed to be able to use PRESCOTT.</p>
</section>
<section id="preparation-of-the-environment-and-installation-of-esgemme">
<h2>Preparation of the environment and installation of ESGEMME<a class="headerlink" href="#preparation-of-the-environment-and-installation-of-esgemme" title="Permalink to this heading"></a></h2>
<h2>Preparation of the environment and installation of PRESCOTT<a class="headerlink" href="#preparation-of-the-environment-and-installation-of-esgemme" title="Permalink to this heading"></a></h2>
<p>Step by step installation on Ubuntu 22.04</p>
<p>Prepare your environment and install the required packages:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo apt-get update --fix-missing <span class="o">&amp;&amp;</span> <span class="se">\</span>
......@@ -184,25 +184,25 @@ your system. Save the file and exit. Then,</p>
</div>
<p>#</p>
<blockquote>
<div><p>cd ESGEMME</p>
<div><p>cd PRESCOTT</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.!
<p>#Download PRESCOTT from <a class="reference external" href="http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT">http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT</a> repository and go inside the PRESCOTT folder.!
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
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git clone http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT.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
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git clone -b development http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT.git
</pre></div>
</div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> ESGEMME
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> PRESCOTT
</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>
<p>Inside ESGEMME/esgemme folder, there is an important file called default.conf.
This file contains essential parameters of ESGEMME, such as paths of
<p>Inside PRESCOTT/esgemme folder, there is an important file called default.conf.
This file contains essential parameters of PRESCOTT, such as paths of
external parts, default internal parameters. etc. You have to correct the Software section of this
file according to your system.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip3 install -e . <span class="o">&amp;&amp;</span><span class="se">\</span>
......
docs/_build/html/search.html
......@@ -44,8 +44,8 @@
</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="docker.html">Using ESGEMME via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESGEMME Output</a></li>
<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="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>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
</ul>
......
docs/_build/latex/esgemme.aux
......@@ -20,11 +20,11 @@
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......@@ -39,13 +39,13 @@
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......@@ -64,8 +64,8 @@
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......
docs/_build/latex/esgemme.fls
PWD /home/tekpinar/research/lcqb/ESGEMME/docs/_build/latex
PWD /home/tekpinar/research/lcqb/PRESCOTT/docs/_build/latex
INPUT /etc/texmf/web2c/texmf.cnf
INPUT /usr/share/texmf/web2c/texmf.cnf
INPUT /usr/share/texlive/texmf-dist/web2c/texmf.cnf
......
docs/_build/latex/esgemme.tex
......@@ -85,7 +85,7 @@
\sphinxstepscope
\chapter{Using ESGEMME via Docker}
\chapter{Using PRESCOTT via Docker}
\label{\detokenize{docker:using-esgemme-via-docker}}\label{\detokenize{docker::doc}}
\section{Requirements}
......@@ -114,19 +114,19 @@ mkdir docker\PYGZhy{}tutorial
\section{Getting the example input data}
\label{\detokenize{docker:getting-the-example-input-data}}
\sphinxAtStartPar
Let’s download the sample data provided in the ESGEMME repository for
Let’s download the sample data provided in the PRESCOTT repository for
this exercise. First, we will download the multiple sequence alignment
file in fasta format:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta
wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta
\end{sphinxVerbatim}
\sphinxAtStartPar
If you don’t have wget, you can try the same command with curl:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta \PYGZgt{}aliBLAT.fasta
curl http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta \PYGZgt{}aliBLAT.fasta
\end{sphinxVerbatim}
\sphinxAtStartPar
......@@ -136,7 +136,7 @@ Please verify that the aliBLAT.fasta file is in the folder.
Now, we will download the PDB (Protein Databank) file for BLAT:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/blat\PYGZhy{}af2.pdb
wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/blat\PYGZhy{}af2.pdb
\end{sphinxVerbatim}
......@@ -204,10 +204,10 @@ esgemme aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta \PYGZhy{}\PYGZhy{}pdbfile blat\PY
If you are interested in only a bunch of single point mutations,
you have to prepare a mut file. The format is a simple text file and
each line contains a single point mutation such as D26A….
Fortunately, we have an example mut in data folder of ESGEMME repository.
Fortunately, we have an example mut in data folder of PRESCOTT repository.
\begin{sphinxVerbatim}[commandchars=\\\{\}]
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/master/data/Stiffler\PYGZus{}2015\PYGZus{}BLAT\PYGZus{}ECOLX.mut
wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/master/data/Stiffler\PYGZus{}2015\PYGZus{}BLAT\PYGZus{}ECOLX.mut
\end{sphinxVerbatim}
\sphinxAtStartPar
......@@ -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. ESGEMME can
Sometimes, we need to see effects of double or triple mutations. PRESCOTT can
perform calculations if you provide a mut file. In this case, the mut file must
have the following format:
......@@ -258,13 +258,13 @@ mutation and its predicted effect, separated by a space.
\sphinxstepscope
\chapter{Analyzing and Modifying the ESGEMME Output}
\chapter{Analyzing and Modifying the PRESCOTT Output}
\label{\detokenize{analysis:analyzing-and-modifying-the-esgemme-output}}\label{\detokenize{analysis::doc}}
\section{Raw ESGEMME Scores and Their Interpretation}
\section{Raw PRESCOTT Scores and Their Interpretation}
\label{\detokenize{analysis:raw-esgemme-scores-and-their-interpretation}}
\sphinxAtStartPar
There is not a hardcoded limit for raw ESGEMME scores. However, the values
There is not a hardcoded limit for raw PRESCOTT scores. However, the values
range between {[}\sphinxhyphen{}12, 2{]} generally. The lower values mean the mutations is impactful,
while values close to 0 means the mutation does not have any significant impact.
......@@ -276,7 +276,7 @@ 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, ESGEMME will only output the combined (independent
By default, PRESCOTT will only output the combined (independent
and epistatic) scores*:
\sphinxAtStartPar
......@@ -401,7 +401,7 @@ terminal.
Unfortunately, a3m file is not in fasta format and it contains gap columns.
We have to clean those gaps. We can do that with a GUI program like Ugene
or Jalview. However, it is a labor intensive procedure. Here, I will use a
small tool that I developed and added to the ESGEMME docker image that I created.
small tool that I developed and added to the PRESCOTT docker image that I created.
\item {}
\sphinxAtStartPar
......@@ -454,7 +454,7 @@ awk \PYG{l+s+s1}{\PYGZsq{}BEGIN\PYGZob{}FS=\PYGZdq{} \PYGZdq{}\PYGZcb{}\PYGZob{}
\end{quote}
\sphinxAtStartPar
Congratulations! Now, you have all the input files required for ESGEMME:
Congratulations! Now, you have all the input files required for PRESCOTT:
I. An input MSA: AKE\_nogaps\_short\_names.fasta
II. An input PDB: myprotein.pdb
......@@ -464,8 +464,8 @@ II. An input PDB: myprotein.pdb
\chapter{Installation}
\label{\detokenize{installation:installation}}\label{\detokenize{installation::doc}}
\sphinxAtStartPar
ESGEMME is implemented in Python 3 and R. It has been tested only on
Linux. Since ESGEMME has many dependencies, we recommend using our web
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, here comes the
steps required to install it from the source.
......@@ -473,7 +473,7 @@ steps required to install it from the source.
\section{Installing the dependencies:}
\label{\detokenize{installation:installing-the-dependencies}}
\sphinxAtStartPar
ESGEMME has the following external dependencies:
PRESCOTT has the following external dependencies:
\begin{itemize}
\item {}
\sphinxAtStartPar
......@@ -517,10 +517,10 @@ Then, source the saved .profile so that the environment variable will be taken i
\end{sphinxVerbatim}
\sphinxAtStartPar
JET2 is essential and it should be installed to be able to use ESGEMME.
JET2 is essential and it should be installed to be able to use PRESCOTT.
\section{Preparation of the environment and installation of ESGEMME}
\section{Preparation of the environment and installation of PRESCOTT}
\label{\detokenize{installation:preparation-of-the-environment-and-installation-of-esgemme}}
\sphinxAtStartPar
Step by step installation on Ubuntu 22.04
......@@ -621,34 +621,34 @@ your system. Save the file and exit. Then,
\begin{quote}
\sphinxAtStartPar
cd ESGEMME
cd PRESCOTT
\end{quote}
\sphinxAtStartPar
\#Download ESGEMME from \sphinxurl{http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME} repository and go inside the ESGEMME folder.!
\#Download PRESCOTT from \sphinxurl{http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT} repository and go inside the PRESCOTT folder.!
You can download the master version using command line as follows:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
git clone http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
git clone http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT.git
\end{sphinxVerbatim}
\sphinxAtStartPar
If you would like the development version:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
git clone \PYGZhy{}b development http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
git clone \PYGZhy{}b development http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT.git
\end{sphinxVerbatim}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
\PYG{n+nb}{cd} ESGEMME
\PYG{n+nb}{cd} PRESCOTT
\end{sphinxVerbatim}
\section{Configuring default.conf file}
\label{\detokenize{installation:configuring-default-conf-file}}
\sphinxAtStartPar
Inside ESGEMME/esgemme folder, there is an important file called default.conf.
This file contains essential parameters of ESGEMME, such as paths of
Inside PRESCOTT/esgemme folder, there is an important file called default.conf.
This file contains essential parameters of PRESCOTT, such as paths of
external parts, default internal parameters. etc. You have to correct the Software section of this
file according to your system.
......
docs/_build/latex/esgemme.toc
\babel@toc {english}{}\relax
\contentsline {chapter}{\numberline {1}Using ESGEMME via Docker}{1}{chapter.1}%
\contentsline {chapter}{\numberline {1}Using PRESCOTT 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}%
......@@ -7,14 +7,14 @@
\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 ESGEMME Output}{5}{chapter.2}%
\contentsline {section}{\numberline {2.1}Raw ESGEMME Scores and Their Interpretation}{5}{section.2.1}%
\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 ESGEMME}{9}{section.4.2}%
\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}%
docs/analysis.rst
Analyzing and Modifying the ESGEMME Output
Analyzing and Modifying the PRESCOTT Output
==========================================
Raw ESGEMME Scores and Their Interpretation
Raw PRESCOTT Scores and Their Interpretation
-------------------------------------------
There is not a hardcoded limit for raw ESGEMME scores. However, the values
There is not a hardcoded limit for raw PRESCOTT scores. However, the values
range between [-12, 2] generally. The lower values mean the mutations is impactful,
while values close to 0 means the mutation does not have any significant impact.
......@@ -13,7 +13,7 @@ it is not always the case.
Entire Single Point Mutation Landscape Calculations
---------------------------------------------------
By default, ESGEMME will only output the combined (independent
By default, PRESCOTT will only output the combined (independent
and epistatic) scores*:
There are three output files:
......
docs/docker.rst
Using ESGEMME via Docker
Using PRESCOTT via Docker
========================
Requirements
......@@ -23,19 +23,19 @@ folder:
Getting the example input data
------------------------------
Let’s download the sample data provided in the ESGEMME repository for
Let’s download the sample data provided in the PRESCOTT repository for
this exercise. First, we will download the multiple sequence alignment
file in fasta format:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta
wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta
If you don’t have wget, you can try the same command with curl:
.. code:: bash
curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta >aliBLAT.fasta
curl http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/aliBLAT.fasta >aliBLAT.fasta
Please verify that the aliBLAT.fasta file is in the folder.
......@@ -43,7 +43,7 @@ Now, we will download the PDB (Protein Databank) file for BLAT:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/blat-af2.pdb
wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/8d766d4d11af0e93c9da8fc2c5cc1bfc457d2936/data/blat-af2.pdb
Single point mutation calculations
----------------------------------
......@@ -100,11 +100,11 @@ Predicting the effect of a subset of single point mutations
If you are interested in only a bunch of single point mutations,
you have to prepare a mut file. The format is a simple text file and
each line contains a single point mutation such as D26A....
Fortunately, we have an example mut in data folder of ESGEMME repository.
Fortunately, we have an example mut in data folder of PRESCOTT repository.
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/master/data/Stiffler_2015_BLAT_ECOLX.mut
wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/master/data/Stiffler_2015_BLAT_ECOLX.mut
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:
......@@ -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. ESGEMME can
Sometimes, we need to see effects of double or triple mutations. PRESCOTT can
perform calculations if you provide a mut file. In this case, the mut file must
have the following format:
......
docs/input-preparation.rst
......@@ -36,7 +36,7 @@ structure is to use Colabfold. Let's do this step by step:
7. Unfortunately, a3m file is not in fasta format and it contains gap columns.
We have to clean those gaps. We can do that with a GUI program like Ugene
or Jalview. However, it is a labor intensive procedure. Here, I will use a
small tool that I developed and added to the ESGEMME docker image that I created.
small tool that I developed and added to the PRESCOTT docker image that I created.
8. Start the docker image with the following command:
......@@ -75,7 +75,7 @@ a3m and fasta files are too long. We have to shorten them. We can do that with
# Recheck this command if you can remove extra >
Congratulations! Now, you have all the input files required for ESGEMME:
Congratulations! Now, you have all the input files required for PRESCOTT:
I. An input MSA: AKE_nogaps_short_names.fasta
II. An input PDB: myprotein.pdb
......
docs/installation.rst
Installation
------------
ESGEMME is implemented in Python 3 and R. It has been tested only on
Linux. Since ESGEMME has many dependencies, we recommend using our web
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, here comes the
steps required to install it from the source.
Installing the dependencies:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ESGEMME has the following external dependencies:
PRESCOTT has the following external dependencies:
* Joint Evolutionary Trees: http://www.lcqb.upmc.fr/JET2/ and its dependencies:
......@@ -38,9 +38,9 @@ Then, source the saved .profile so that the environment variable will be taken i
source ~/.profile
JET2 is essential and it should be installed to be able to use ESGEMME.
JET2 is essential and it should be installed to be able to use PRESCOTT.
Preparation of the environment and installation of ESGEMME
Preparation of the environment and installation of PRESCOTT
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step by step installation on Ubuntu 22.04
......@@ -131,30 +131,30 @@ your system. Save the file and exit. Then,
#
cd ESGEMME
cd PRESCOTT
#Download ESGEMME from http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME repository and go inside the ESGEMME folder.!
#Download PRESCOTT from http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT repository and go inside the PRESCOTT folder.!
You can download the master version using command line as follows:
.. code:: bash
git clone http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
git clone http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT.git
If you would like the development version:
.. code:: bash
git clone -b development http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
git clone -b development http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT.git
.. code:: bash
cd ESGEMME
cd PRESCOTT
Configuring default.conf file
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Inside ESGEMME/esgemme folder, there is an important file called default.conf.
This file contains essential parameters of ESGEMME, such as paths of
Inside PRESCOTT/esgemme folder, there is an important file called default.conf.
This file contains essential parameters of PRESCOTT, such as paths of
external parts, default internal parameters. etc. You have to correct the Software section of this
file according to your system.
......
esgemme/computePred.R
......@@ -6,13 +6,13 @@
# Usage: Rscript --save computePred.R XXXX
library("seqinr")
#source(paste(Sys.getenv("ESGEMME_PATH"),"/pred.R",sep=""))
#source(paste(Sys.getenv("PRESCOTT_PATH"),"/pred.R",sep=""))
source("pred.R")
# amino acid full alphabet
aa = c("a","c","d","e","f","g","h","i","k","l","m","n","p","q","r","s","t","v","w","y")
# # BLOSUM62 matrix
# blosum62p = as.matrix(read.table(paste0(Sys.getenv("ESGEMME_PATH"),"/data/blosum62p.txt"),row.names=1))
# blosum62p = as.matrix(read.table(paste0(Sys.getenv("PRESCOTT_PATH"),"/data/blosum62p.txt"),row.names=1))
# bgp = blosum62p[order(rownames(blosum62p)),order(colnames(blosum62p))]
# bg = apply(bgp,1,sum)
......
esgemme/esgemme.py
......@@ -203,7 +203,7 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
chainID = chains[0]
# esgemme_path = os.path.expandvars ('$ESGEMME_PATH')
# esgemme_path = os.path.expandvars ('$PRESCOTT_PATH')
# shutil.copy2(os.path.join(esgemme_path, "default.conf"), os.getcwd())
# esgemme_default_conf_path = importlib.resources.path('esgemme', 'default.conf')
# print(esgemme_default_conf_path)
......@@ -328,10 +328,10 @@ def launchPred(prot,inAli,mutFile, normWeightMode, alphabet):
shutil.copy2(esgemme_alphabet, os.getcwd())
if (mutFile!=''):
# rcmd="Rscript --save $ESGEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
# rcmd="Rscript --save $PRESCOTT_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
rcmd="Rscript --save computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
else:
# rcmd="Rscript --save $ESGEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
# rcmd="Rscript --save $PRESCOTT_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
rcmd="Rscript --save computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
print("\nRunning Rscript with following arguments: \n"+rcmd)
......@@ -897,7 +897,7 @@ def parse_command_line():
parser = argparse.ArgumentParser(
prog="esgemme",
description="""
ESGEMME (Evolutionary and Structural Global Epistasis Model for predicting Mutational Effects)
PRESCOTT (Evolutionary and Structural Global Epistasis Model for predicting Mutational Effects)
is a tool to predict mutational outcomes based on sequence and structure analysis
""",
epilog="""
......@@ -1006,7 +1006,7 @@ def parse_command_line():
# Check flag arguments
if args.input is None:
parser.error("ESGEMME requires an input alignment.")
parser.error("PRESCOTT requires an input alignment.")
return args
......@@ -1457,7 +1457,7 @@ def main():
toc = time.perf_counter()
print(f"ESGEMME computation finished in {toc - tic:0.4f} seconds!")
print(f"PRESCOTT computation finished in {toc - tic:0.4f} seconds!")
if (__name__ == '__main__'):
main()
......
esgemme/pred.R
......@@ -174,7 +174,7 @@ computeNbSeqs<-function(mat,gap=FALSE){
# }
computeNbSeqsAlph<-function(nbSeqs,alphabet){
# path=paste(Sys.getenv("ESGEMME_PATH"),"/data/alphabets/",sep="")
# path=paste(Sys.getenv("PRESCOTT_PATH"),"/data/alphabets/",sep="")
# AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
AA = read.table(paste(alphabet,".txt",sep=""))$V1
......@@ -212,7 +212,7 @@ readMut<-function(fname){
}
which.class<-function(a,alphabet){
# path=paste(Sys.getenv("ESGEMME_PATH"),"/data/alphabets/",sep="")
# path=paste(Sys.getenv("PRESCOTT_PATH"),"/data/alphabets/",sep="")
# AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
AA = read.table(paste(alphabet,".txt",sep=""))$V1
for(Let in AA){
......
examples/example-esgemme-script.sh
......@@ -17,7 +17,7 @@ elif [ "$1" == "jetoff" ]
then
# If you have your own JET2 score file, you can turn off JET2 as follows:
# In ../tests folder, you can find a sample JET2 file called BLAT_jet.res
echo "Running ESGEMME with a user-provided alignment file."
echo "Running PRESCOTT with a user-provided alignment file."
echo "Using a previously produced prot_jet.res file to check reproducibility!"
esgemme ../data/aliBLAT.fasta -f ../data/aliBLAT.fasta --jetfile ../data/BLAT_jet.res
......
setup.py
......@@ -32,7 +32,7 @@ from esgemme import __version__ as cp_vers
setup(name='esgemme',
version=cp_vers,
description="ESGEMME: A Python program to predict mutational effects of proteins.",
description="PRESCOTT: A Python program to predict mutational effects of proteins.",
long_description=open('README.md').read(),
long_description_content_type="text/markdown",
author="Mustafa Tekpinar",
......
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