Removed ESGEMME_PATH dependecy for R files.

Since esgemme calls two R scripts, namely pred.R and computePred.R, to do the calculations, I added them as package resource. They are copied to the folder where ESGEMME is initiated. I'm trying to remove this kind of path dependencies to make the program automatically installable and portable.

Removed ESGEMME_PATH dependecy for R files.
Since esgemme calls two R scripts, namely pred.R and computePred.R, to do the calculations, I added them as package resource. They are copied to the folder where ESGEMME is initiated. I'm trying to remove this kind of path dependencies to make the program automatically installable and portable.
0c7fe1f3 · Mustafa Tekpinar · a17f0f90 · 0c7fe1f3 · 0c7fe1f3 · 0c7fe1f3
Commit 0c7fe1f3 authored Jun 08, 2023 by Mustafa Tekpinar
26 changed files
--- a/Dockerfile
+++ b/Dockerfile
@@ -15,7 +15,7 @@ COPY ./ESGEMME/requirements.txt ./ESGEMME/requirements.txt
 COPY ./ESGEMME/README.md ./ESGEMME/README.md 
 COPY ./ESGEMME/pred.R ./ESGEMME/pred.R
 COPY ./ESGEMME/computePred.R ./ESGEMME/computePred.R
-COPY ./ESGEMME/default.conf ./ESGEMME/default.conf
+COPY ./ESGEMME/esgemme/default.conf ./ESGEMME/esgemme/default.conf
 COPY ./ESGEMME/data/ ./ESGEMME/data/
 COPY ./ESGEMME/examples/ ./ESGEMME/examples/
 COPY ./demust/ ./demust/

--- a/docs/_build/doctrees/analysis.doctree
+++ b/docs/_build/doctrees/analysis.doctree
--- a/docs/_build/doctrees/environment.pickle
+++ b/docs/_build/doctrees/environment.pickle
--- a/docs/_build/html/_sources/analysis.rst.txt
+++ b/docs/_build/html/_sources/analysis.rst.txt
-Analyzing the ESGEMME output
+Analyzing and Modifying the ESGEMME Output
----------------------------
+==========================================
-By default, ESGEMME will output the following files: \*
+Raw ESGEMME Scores and Their Interpretation
-myProt_normPred_evolEpi.txt \* myProt_normPred_evolInd.txt \*
+-------------------------------------------
-myProt_normPred_evolCombi.txt
+There is not a hardcoded limit for raw ESGEMME scores. However, the values
+range between [-12, 2] generally. The lower values mean the mutations is impactful, 
-The most important output file is **myProt_normPred_evolCombi.txt**. The
+while values close to 0 means the mutation does not have any significant impact.
-values of interest are the normalized predictions (normPred). Each file
-contains a 20 x n matrix, where n is the number of positions (columns) in the
+We should note that most of the 'impactful' mutations are deleterious but 
-query sequence. If the user provides her/his own list of mutations, then
+it is not always the case. 
-only the global epistatic model will be run and the output file will
-contain 2 columns, the first one with the mutations, the second one with
+Entire Single Point Mutation Landscape Calculations
-the normalized predicted effects.
+---------------------------------------------------
+By default, ESGEMME will only output the combined (independent
+and epistatic) scores*: 
+There are three output files:
+#. myProt_normPred_evolCombi.txt
+    myProt is the short name in the MSA file for your protein. The 
+    'myProt_normPred_evolCombi.txt' file contains 20 rows (for 20 amino acids 
+    in alphabetical order) and L columns, where L is the number of amino acids 
+    in your protein of interest. Since this file is horizontal, it is easy to 
+    read it in R or Python but difficult to find the mutations you are interested.
+#. myProt_normPred_evolCombiTransposed.txt 
+    As the name implies, this is the transposed version of the combined results.
+    It is easier to find the mutations you are interested in this file. Just 
+    check the row corresponding to the mutation.
+#. myProt_normPred_evolCombi.Preparing
+    This is the image file of the combined results. It selects 'Oranges_r'
+    matplotlib color map by default. You can change it by adding '--colormap turbo_r'
+    for a more fancy look during the esgemme call. It --colormap argument accepts
+    all the color maps in matplotlib.
+Note*: If you want to see epistatic and independent contributions as well, 
+you should add '--verbose true' argument while calling esgemme. 
+Selected Single Point or Multiple Point Mutation Calculations
+-------------------------------------------------------------
+Since you used a mutation file to predict mutations, you will have your combined (epistatic+independent) 
+results in the same format, such as :
+*. myProt_normPred_evolCombi.txt:
+    A2C -6.23
+    A2D -1.23
+    .
+    .
+    .
+    D286F -0.23
--- a/docs/_build/html/analysis.html
+++ b/docs/_build/html/analysis.html
@@ -4,7 +4,7 @@
  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Analyzing the ESGEMME output &mdash; esgemme 1.3.0 documentation</title>
+  <title>Analyzing and Modifying the ESGEMME Output &mdash; esgemme 1.3.0 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]>
@@ -45,7 +45,12 @@
              <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 current"><a class="current reference internal" href="#">Analyzing the ESGEMME output</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-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>
+</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>
@@ -64,7 +69,7 @@
          <div role="navigation" aria-label="Page navigation">
  <ul class="wy-breadcrumbs">
      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
-      <li class="breadcrumb-item active">Analyzing the ESGEMME output</li>
+      <li class="breadcrumb-item active">Analyzing and Modifying the ESGEMME Output</li>
      <li class="wy-breadcrumbs-aside">
            <a href="_sources/analysis.rst.txt" rel="nofollow"> View page source</a>
      </li>
@@ -74,18 +79,64 @@
          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
           <div itemprop="articleBody">
-  <section id="analyzing-the-esgemme-output">
+  <section id="analyzing-and-modifying-the-esgemme-output">
-<h1>Analyzing the ESGEMME output<a class="headerlink" href="#analyzing-the-esgemme-output" title="Permalink to this heading"></a></h1>
+<h1>Analyzing and Modifying the ESGEMME Output<a class="headerlink" href="#analyzing-and-modifying-the-esgemme-output" title="Permalink to this heading"></a></h1>
-<p>By default, ESGEMME will output the following files: *
+<section id="raw-esgemme-scores-and-their-interpretation">
-myProt_normPred_evolEpi.txt * myProt_normPred_evolInd.txt *
+<h2>Raw ESGEMME Scores and Their Interpretation<a class="headerlink" href="#raw-esgemme-scores-and-their-interpretation" title="Permalink to this heading"></a></h2>
-myProt_normPred_evolCombi.txt</p>
+<p>There is not a hardcoded limit for raw ESGEMME scores. However, the values
-<p>The most important output file is <strong>myProt_normPred_evolCombi.txt</strong>. The
+range between [-12, 2] generally. The lower values mean the mutations is impactful,
-values of interest are the normalized predictions (normPred). Each file
+while values close to 0 means the mutation does not have any significant impact.</p>
-contains a 20 x n matrix, where n is the number of positions (columns) in the
+<p>We should note that most of the ‘impactful’ mutations are deleterious but
-query sequence. If the user provides her/his own list of mutations, then
+it is not always the case.</p>
-only the global epistatic model will be run and the output file will
+</section>
-contain 2 columns, the first one with the mutations, the second one with
+<section id="entire-single-point-mutation-landscape-calculations">
-the normalized predicted effects.</p>
+<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
+and epistatic) scores*:</p>
+<p>There are three output files:</p>
+<ol class="arabic">
+<li><p>myProt_normPred_evolCombi.txt</p>
+<blockquote>
+<div><p>myProt is the short name in the MSA file for your protein. The
+‘myProt_normPred_evolCombi.txt’ file contains 20 rows (for 20 amino acids
+in alphabetical order) and L columns, where L is the number of amino acids
+in your protein of interest. Since this file is horizontal, it is easy to
+read it in R or Python but difficult to find the mutations you are interested.</p>
+</div></blockquote>
+</li>
+<li><p>myProt_normPred_evolCombiTransposed.txt</p>
+<blockquote>
+<div><p>As the name implies, this is the transposed version of the combined results.
+It is easier to find the mutations you are interested in this file. Just
+check the row corresponding to the mutation.</p>
+</div></blockquote>
+</li>
+<li><p>myProt_normPred_evolCombi.Preparing</p>
+<blockquote>
+<div><p>This is the image file of the combined results. It selects ‘Oranges_r’
+matplotlib color map by default. You can change it by adding ‘–colormap turbo_r’
+for a more fancy look during the esgemme call. It –colormap argument accepts
+all the color maps in matplotlib.</p>
+</div></blockquote>
+</li>
+</ol>
+<p>Note*: If you want to see epistatic and independent contributions as well,
+you should add ‘–verbose true’ argument while calling esgemme.</p>
+</section>
+<section id="selected-single-point-or-multiple-point-mutation-calculations">
+<h2>Selected Single Point or Multiple Point Mutation Calculations<a class="headerlink" href="#selected-single-point-or-multiple-point-mutation-calculations" title="Permalink to this heading"></a></h2>
+<p>Since you used a mutation file to predict mutations, you will have your combined (epistatic+independent)
+results in the same format, such as :</p>
+<dl class="simple">
+<dt><a href="#id1"><span class="problematic" id="id2">*</span></a>. myProt_normPred_evolCombi.txt:</dt><dd><p>A2C -6.23
+A2D -1.23
+.
+.
+.
+D286F -0.23</p>
+</dd>
+</dl>
+</section>
 </section>

--- a/docs/_build/html/docker.html
+++ b/docs/_build/html/docker.html
@@ -19,7 +19,7 @@
    <script src="_static/js/theme.js"></script>
    <link rel="index" title="Index" href="genindex.html" />
    <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Analyzing the ESGEMME output" href="analysis.html" />
+    <link rel="next" title="Analyzing and Modifying the ESGEMME Output" href="analysis.html" />
    <link rel="prev" title="Welcome to esgemme’s documentation!" href="index.html" /> 
 </head>
@@ -56,7 +56,8 @@
 <li class="toctree-l2"><a class="reference internal" href="#running-several-jobs-using-docker">Running several jobs using docker</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing the ESGEMME output</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="analysis.html#raw-esgemme-scores-and-their-interpretation">Raw ESGEMME Scores and Their Interpretation</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>
@@ -210,7 +211,7 @@ mutation and its predicted effect, separated by a space.</p>
          </div>
          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
        <a href="index.html" class="btn btn-neutral float-left" title="Welcome to esgemme’s documentation!" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="analysis.html" class="btn btn-neutral float-right" title="Analyzing the ESGEMME output" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="analysis.html" class="btn btn-neutral float-right" title="Analyzing and Modifying the ESGEMME Output" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
    </div>
  <hr/>

--- a/docs/_build/html/genindex.html
+++ b/docs/_build/html/genindex.html
@@ -42,7 +42,7 @@
              <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 the ESGEMME output</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="input-preparation.html">Preparing Your Own Input</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 </ul>

--- a/docs/_build/html/index.html
+++ b/docs/_build/html/index.html
@@ -44,7 +44,7 @@
              <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 the ESGEMME output</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="input-preparation.html">Preparing Your Own Input</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 </ul>
@@ -86,7 +86,12 @@
 <li class="toctree-l2"><a class="reference internal" href="docker.html#running-several-jobs-using-docker">Running several jobs using docker</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing the ESGEMME output</a></li>
+<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESGEMME Output</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="analysis.html#raw-esgemme-scores-and-their-interpretation">Raw ESGEMME 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>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="input-preparation.html">Preparing Your Own Input</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="input-preparation.html#preparing-your-input-msa-and-pdb-with-colabfold">Preparing Your Input MSA and PDB with Colabfold</a></li>
 </ul>

--- a/docs/_build/html/input-preparation.html
+++ b/docs/_build/html/input-preparation.html
@@ -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" />
-    <link rel="prev" title="Analyzing the ESGEMME output" href="analysis.html" /> 
+    <link rel="prev" title="Analyzing and Modifying the ESGEMME Output" href="analysis.html" /> 
 </head>
 <body class="wy-body-for-nav"> 
@@ -45,7 +45,8 @@
              <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 the ESGEMME output</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="analysis.html#raw-esgemme-scores-and-their-interpretation">Raw ESGEMME Scores and Their Interpretation</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>
@@ -141,7 +142,7 @@ II. An input PDB: myprotein.pdb</p>
           </div>
          </div>
          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="analysis.html" class="btn btn-neutral float-left" title="Analyzing the ESGEMME output" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="analysis.html" class="btn btn-neutral float-left" title="Analyzing and Modifying the ESGEMME Output" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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    </div>

--- a/docs/_build/html/installation.html
+++ b/docs/_build/html/installation.html
@@ -44,7 +44,8 @@
              <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 the ESGEMME output</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="analysis.html#raw-esgemme-scores-and-their-interpretation">Raw ESGEMME Scores and Their Interpretation</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>

--- a/docs/_build/html/objects.inv
+++ b/docs/_build/html/objects.inv
--- a/docs/_build/html/search.html
+++ b/docs/_build/html/search.html
@@ -45,7 +45,7 @@
              <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 the ESGEMME output</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="input-preparation.html">Preparing Your Own Input</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 </ul>

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\ No newline at end of file
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 \title{esgemme}
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 \author{Mustafa Tekpinar}
 \newcommand{\sphinxlogo}{\vbox{}}
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 \sphinxstepscope
-\chapter{Analyzing the ESGEMME output}
+\chapter{Analyzing and Modifying the ESGEMME Output}
-\label{\detokenize{analysis:analyzing-the-esgemme-output}}\label{\detokenize{analysis::doc}}
+\label{\detokenize{analysis:analyzing-and-modifying-the-esgemme-output}}\label{\detokenize{analysis::doc}}
+\section{Raw ESGEMME 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
+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.
+\sphinxAtStartPar
+We should note that most of the ‘impactful’ mutations are deleterious but
+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
+and epistatic) scores*:
+\sphinxAtStartPar
+There are three output files:
+\begin{enumerate}
+\sphinxsetlistlabels{\arabic}{enumi}{enumii}{}{.}%
+\item {} 
 \sphinxAtStartPar
-By default, ESGEMME will output the following files: *
-myProt\_normPred\_evolEpi.txt * myProt\_normPred\_evolInd.txt *
 myProt\_normPred\_evolCombi.txt
+\begin{quote}
 \sphinxAtStartPar
-The most important output file is \sphinxstylestrong{myProt\_normPred\_evolCombi.txt}. The
+myProt is the short name in the MSA file for your protein. The
-values of interest are the normalized predictions (normPred). Each file
+‘myProt\_normPred\_evolCombi.txt’ file contains 20 rows (for 20 amino acids
-contains a 20 x n matrix, where n is the number of positions (columns) in the
+in alphabetical order) and L columns, where L is the number of amino acids
-query sequence. If the user provides her/his own list of mutations, then
+in your protein of interest. Since this file is horizontal, it is easy to
-only the global epistatic model will be run and the output file will
+read it in R or Python but difficult to find the mutations you are interested.
-contain 2 columns, the first one with the mutations, the second one with
+\end{quote}
-the normalized predicted effects.
+\item {} 
+\sphinxAtStartPar
+myProt\_normPred\_evolCombiTransposed.txt
+\begin{quote}
+\sphinxAtStartPar
+As the name implies, this is the transposed version of the combined results.
+It is easier to find the mutations you are interested in this file. Just
+check the row corresponding to the mutation.
+\end{quote}
+\item {} 
+\sphinxAtStartPar
+myProt\_normPred\_evolCombi.Preparing
+\begin{quote}
+\sphinxAtStartPar
+This is the image file of the combined results. It selects ‘Oranges\_r’
+matplotlib color map by default. You can change it by adding ‘\textendash{}colormap turbo\_r’
+for a more fancy look during the esgemme call. It \textendash{}colormap argument accepts
+all the color maps in matplotlib.
+\end{quote}
+\end{enumerate}
+\sphinxAtStartPar
+Note*: If you want to see epistatic and independent contributions as well,
+you should add ‘\textendash{}verbose true’ argument while calling esgemme.
+\section{Selected Single Point or Multiple Point Mutation Calculations}
+\label{\detokenize{analysis:selected-single-point-or-multiple-point-mutation-calculations}}
+\sphinxAtStartPar
+Since you used a mutation file to predict mutations, you will have your combined (epistatic+independent)
+results in the same format, such as :
+\begin{description}
+\sphinxlineitem{{\color{red}\bfseries{}*}. myProt\_normPred\_evolCombi.txt:}
+\sphinxAtStartPar
+A2C \sphinxhyphen{}6.23
+A2D \sphinxhyphen{}1.23
+.
+.
+.
+D286F \sphinxhyphen{}0.23
+\end{description}
 \sphinxstepscope

--- a/docs/_build/latex/esgemme.toc
+++ b/docs/_build/latex/esgemme.toc
@@ -7,7 +7,10 @@
 \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 the ESGEMME output}{5}{chapter.2}%
+\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 {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}%

--- a/docs/analysis.rst
+++ b/docs/analysis.rst
-Analyzing the ESGEMME output
+Analyzing and Modifying the ESGEMME Output
----------------------------
+==========================================
-By default, ESGEMME will output the following files: \*
+Raw ESGEMME Scores and Their Interpretation
-myProt_normPred_evolEpi.txt \* myProt_normPred_evolInd.txt \*
+-------------------------------------------
-myProt_normPred_evolCombi.txt
+There is not a hardcoded limit for raw ESGEMME scores. However, the values
+range between [-12, 2] generally. The lower values mean the mutations is impactful, 
-The most important output file is **myProt_normPred_evolCombi.txt**. The
+while values close to 0 means the mutation does not have any significant impact.
-values of interest are the normalized predictions (normPred). Each file
-contains a 20 x n matrix, where n is the number of positions (columns) in the
+We should note that most of the 'impactful' mutations are deleterious but 
-query sequence. If the user provides her/his own list of mutations, then
+it is not always the case. 
-only the global epistatic model will be run and the output file will
-contain 2 columns, the first one with the mutations, the second one with
+Entire Single Point Mutation Landscape Calculations
-the normalized predicted effects.
+---------------------------------------------------
+By default, ESGEMME will only output the combined (independent
+and epistatic) scores*: 
+There are three output files:
+#. myProt_normPred_evolCombi.txt
+    myProt is the short name in the MSA file for your protein. The 
+    'myProt_normPred_evolCombi.txt' file contains 20 rows (for 20 amino acids 
+    in alphabetical order) and L columns, where L is the number of amino acids 
+    in your protein of interest. Since this file is horizontal, it is easy to 
+    read it in R or Python but difficult to find the mutations you are interested.
+#. myProt_normPred_evolCombiTransposed.txt 
+    As the name implies, this is the transposed version of the combined results.
+    It is easier to find the mutations you are interested in this file. Just 
+    check the row corresponding to the mutation.
+#. myProt_normPred_evolCombi.Preparing
+    This is the image file of the combined results. It selects 'Oranges_r'
+    matplotlib color map by default. You can change it by adding '--colormap turbo_r'
+    for a more fancy look during the esgemme call. It --colormap argument accepts
+    all the color maps in matplotlib.
+Note*: If you want to see epistatic and independent contributions as well, 
+you should add '--verbose true' argument while calling esgemme. 
+Selected Single Point or Multiple Point Mutation Calculations
+-------------------------------------------------------------
+Since you used a mutation file to predict mutations, you will have your combined (epistatic+independent) 
+results in the same format, such as :
+*. myProt_normPred_evolCombi.txt:
+    A2C -6.23
+    A2D -1.23
+    .
+    .
+    .
+    D286F -0.23
--- a/computePred.R
+++ b/computePred.R
@@ -6,15 +6,15 @@
 # Usage: Rscript --save computePred.R XXXX
 library("seqinr")
-source(paste(Sys.getenv("ESGEMME_PATH"),"/pred.R",sep=""))
+#source(paste(Sys.getenv("ESGEMME_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
+# # 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("ESGEMME_PATH"),"/data/blosum62p.txt"),row.names=1))
-bgp = blosum62p[order(rownames(blosum62p)),order(colnames(blosum62p))]
+# bgp = blosum62p[order(rownames(blosum62p)),order(colnames(blosum62p))]
-bg = apply(bgp,1,sum)
+# bg = apply(bgp,1,sum)
 # get arguemnts 
 args = commandArgs(trailingOnly = TRUE)

--- a/esgemme/esgemme.py
+++ b/esgemme/esgemme.py
@@ -310,10 +310,25 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
 # Run Rscript to compute predictions
 def launchPred(prot,inAli,mutFile, normWeightMode, alphabet):
+    # I don't want to have a path dependency here. 
+    # Removing this dependency makes the code more portable.
+    # Therefore, I copy the R scripts that are saved as the 
+    # package resources to the current working directory.
+    source = files('esgemme').joinpath('pred.R')
+    with as_file(source) as esgemme_pred_R_path:
+        shutil.copy2(esgemme_pred_R_path, os.getcwd())
+    source = files('esgemme').joinpath('computePred.R')
+    with as_file(source) as esgemme_computePred_R_path:
+        shutil.copy2(esgemme_computePred_R_path, os.getcwd())
    if (mutFile!=''):
-        rcmd="Rscript --save $ESGEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
+        # rcmd="Rscript --save $ESGEMME_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 $ESGEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
+        rcmd="Rscript --save computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
    print("\nRunning: \n"+rcmd)
    reCode=subprocess.call(rcmd,shell=True)
@@ -363,8 +378,8 @@ def cleanTheMess(prot,bFile,fFile, chainID, verbosity=False):
    if os.path.isfile("caracTest.dat"):
        os.remove("caracTest.dat")
-   if os.path.isfile("default.conf"):
+    if os.path.isfile("default.conf"):
-       os.remove("default.conf")
+        os.remove("default.conf")
    if verbosity == False:
        if os.path.isfile(prot+"_normPred_evolInd.txt"):

--- a/pred.R
+++ b/pred.R
--- a/examples/example-esgemme-script.sh
+++ b/examples/example-esgemme-script.sh
@@ -48,7 +48,7 @@ then
    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
+    demust compare -i ../data/BLAT_ECOLX_Stiffler_2015_experimental.dat --itype singleline -j BLAT_normPred_evolCombi.txt --jtype singleline
 elif [ "$1" == "tjetormax" ]
 then

--- a/setup.py
+++ b/setup.py
@@ -45,7 +45,6 @@ setup(name='esgemme',
          'Environment :: Console',
          'Operating System :: POSIX',
          'Programming Language :: Python :: 3',
-          'Programming Language :: Python :: 3.6',
          'Programming Language :: Python :: 3.7',
          'Programming Language :: Python :: 3.8',
          'Programming Language :: Python :: 3.9',
@@ -65,5 +64,5 @@ setup(name='esgemme',
          ]
      },
      include_package_data=True,
-      package_data={'esgemme':['default.conf']},
+      package_data={'esgemme':['default.conf', 'computePred.R', 'pred.R']},
      )