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.

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/

docs/_build/html/_sources/analysis.rst.txt

-Analyzing the ESGEMME output
-----------------------------
-
-By default, ESGEMME will output the following files: \*
-myProt_normPred_evolEpi.txt \* myProt_normPred_evolInd.txt \*
-myProt_normPred_evolCombi.txt
-
-The most important output file is **myProt_normPred_evolCombi.txt**. The
-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
-query sequence. If the user provides her/his own list of mutations, then
-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
-the normalized predicted effects.
+Analyzing and Modifying the ESGEMME Output
+==========================================
+
+Raw ESGEMME Scores and Their Interpretation
+-------------------------------------------
+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, 
+while values close to 0 means the mutation does not have any significant impact.
+
+We should note that most of the 'impactful' mutations are deleterious but 
+it is not always the case. 
+
+Entire Single Point Mutation Landscape Calculations
+---------------------------------------------------
+
+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
+
+
+
+

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">
-<h1>Analyzing the ESGEMME output<a class="headerlink" href="#analyzing-the-esgemme-output" title="Permalink to this heading"></a></h1>
-<p>By default, ESGEMME will output the following files: *
-myProt_normPred_evolEpi.txt * myProt_normPred_evolInd.txt *
-myProt_normPred_evolCombi.txt</p>
-<p>The most important output file is <strong>myProt_normPred_evolCombi.txt</strong>. The
-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
-query sequence. If the user provides her/his own list of mutations, then
-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
-the normalized predicted effects.</p>
+  <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>
+<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
+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
+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
+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>
 
 

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/>

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>

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>

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>
         <a href="installation.html" class="btn btn-neutral float-right" title="Installation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 

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>

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>

docs/_build/latex/esgemme.aux

@@ -38,11 +38,17 @@
 \newlabel{docker:multiple-point-mutation-calculations}{{1.4}{3}{Multiple point mutation calculations}{section.1.4}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {1.5}Running several jobs using docker}{3}{section.1.5}\protected@file@percent }
 \newlabel{docker:running-several-jobs-using-docker}{{1.5}{3}{Running several jobs using docker}{section.1.5}{}}
-\@writefile{toc}{\contentsline {chapter}{\numberline {2}Analyzing the ESGEMME output}{5}{chapter.2}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{\numberline {2}Analyzing and Modifying the ESGEMME Output}{5}{chapter.2}\protected@file@percent }
 \@writefile{lof}{\addvspace {10\p@ }}
 \@writefile{lot}{\addvspace {10\p@ }}
-\newlabel{analysis:analyzing-the-esgemme-output}{{2}{5}{Analyzing the ESGEMME output}{chapter.2}{}}
-\newlabel{analysis::doc}{{2}{5}{Analyzing the ESGEMME output}{chapter.2}{}}
+\newlabel{analysis:analyzing-and-modifying-the-esgemme-output}{{2}{5}{Analyzing and Modifying the ESGEMME Output}{chapter.2}{}}
+\newlabel{analysis::doc}{{2}{5}{Analyzing and Modifying the ESGEMME Output}{chapter.2}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {2.1}Raw ESGEMME Scores and Their Interpretation}{5}{section.2.1}\protected@file@percent }
+\newlabel{analysis:raw-esgemme-scores-and-their-interpretation}{{2.1}{5}{Raw ESGEMME Scores and Their Interpretation}{section.2.1}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {2.2}Entire Single Point Mutation Landscape Calculations}{5}{section.2.2}\protected@file@percent }
+\newlabel{analysis:entire-single-point-mutation-landscape-calculations}{{2.2}{5}{Entire Single Point Mutation Landscape Calculations}{section.2.2}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {2.3}Selected Single Point or Multiple Point Mutation Calculations}{6}{section.2.3}\protected@file@percent }
+\newlabel{analysis:selected-single-point-or-multiple-point-mutation-calculations}{{2.3}{6}{Selected Single Point or Multiple Point Mutation Calculations}{section.2.3}{}}
 \@writefile{toc}{\contentsline {chapter}{\numberline {3}Preparing Your Own Input}{7}{chapter.3}\protected@file@percent }
 \@writefile{lof}{\addvspace {10\p@ }}
 \@writefile{lot}{\addvspace {10\p@ }}

docs/_build/latex/esgemme.fdb_latexmk

 # Fdb version 3
-["makeindex esgemme.idx"] 1685453958 "esgemme.idx" "esgemme.ind" "esgemme" 1685453959
-  "esgemme.idx" 1685453959 0 d41d8cd98f00b204e9800998ecf8427e "pdflatex"
+["makeindex esgemme.idx"] 1685453958 "esgemme.idx" "esgemme.ind" "esgemme" 1686237775
+  "esgemme.idx" 1686237775 0 d41d8cd98f00b204e9800998ecf8427e "pdflatex"
   (generated)
-  "esgemme.ind"
   "esgemme.ilg"
-["pdflatex"] 1685453959 "esgemme.tex" "esgemme.pdf" "esgemme" 1685453959
+  "esgemme.ind"
+["pdflatex"] 1686237775 "esgemme.tex" "esgemme.pdf" "esgemme" 1686237775
   "/etc/texmf/web2c/texmf.cnf" 1685303669 475 c0e671620eb5563b2130f56340a5fde8 ""
   "/usr/share/texlive/texmf-dist/fonts/map/fontname/texfonts.map" 1577235249 3524 cb3e574dea2d1052e39280babc910dc8 ""
   "/usr/share/texlive/texmf-dist/fonts/tfm/jknappen/ec/ecrm1000.tfm" 1136768653 3584 adb004a0c8e7c46ee66cad73671f37b4 ""
@@ -139,37 +139,37 @@
   "/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd" 1480098840 1160 de7b1cf70edab73c9f1704df2a9fdbbd ""
   "/usr/share/texmf/web2c/texmf.cnf" 1581979058 38841 ce3692aa899bb693b90b87eaa5d4d84e ""
   "/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map" 1685303937 128028 f533b797fba58d231669ea19e894e23e ""
-  "/var/lib/texmf/web2c/pdftex/pdflatex.fmt" 1685303943 4791332 cdca06fe91bc297381d833a8a404c34f ""
-  "esgemme.aux" 1685453959 5380 6ba2642bb60de5c9b9428845f95c5e71 "pdflatex"
-  "esgemme.ind" 1685453958 0 d41d8cd98f00b204e9800998ecf8427e "makeindex esgemme.idx"
-  "esgemme.out" 1685453959 3604 70b9b9c1aed09758e4d1af545c6738b0 "pdflatex"
-  "esgemme.tex" 1685453952 16448 8ac3957ad642260f281f90c676c3a0dd ""
-  "esgemme.toc" 1685453959 1504 2ddd4f41427a60d2ed714388681ed291 "pdflatex"
-  "sphinx.sty" 1685303546 44560 f9fbf51072c954d129c9bd5284cc4ccf ""
-  "sphinxhighlight.sty" 1685453957 7490 72d023191655734567e0798eade2a1f7 ""
-  "sphinxlatexadmonitions.sty" 1685303546 10989 c38302e64c2bb47779f086869b246760 ""
-  "sphinxlatexcontainers.sty" 1685303546 901 d3a3a1b7b2547f47ade2499350b5c420 ""
-  "sphinxlatexgraphics.sty" 1685303546 4840 a9578332b6f3b35e198751fb632c9b79 ""
-  "sphinxlatexindbibtoc.sty" 1685303546 2066 b93f8504d02f6337fde3074b179de55e ""
-  "sphinxlatexlists.sty" 1685303546 5139 c2de2a1d98d3c6ceedfe46505abd3c07 ""
-  "sphinxlatexliterals.sty" 1685303546 46048 2b66269d0ecf11768a14b5de4ddf9051 ""
-  "sphinxlatexnumfig.sty" 1685303546 4532 3633caf84afa1a98e1a060b7868202bb ""
-  "sphinxlatexobjects.sty" 1685303546 9067 1f9a0f04e0268b8abeb7d37165057523 ""
-  "sphinxlatexshadowbox.sty" 1685303546 5066 97a2be0d1dfdc98548b7461f1949b95f ""
-  "sphinxlatexstyleheadings.sty" 1685303546 3445 a1582a5f3b336dcffa71b5ca3d8fc31f ""
-  "sphinxlatexstylepage.sty" 1685303546 3064 abce6c3018a84afee0afb08a431944ea ""
-  "sphinxlatexstyletext.sty" 1685303546 8232 280fdc24a7889c35e545cd62e6cba921 ""
-  "sphinxlatextables.sty" 1685303546 57830 16f2773b765508003aec5d08680f39b9 ""
-  "sphinxmanual.cls" 1685303546 4241 7b0d7a37df7b5715fb0dbd585c52ecdb ""
-  "sphinxmessages.sty" 1685453958 745 3f5fcd6cdd7964ed608767954a8ced6f ""
-  "sphinxoptionsgeometry.sty" 1685303546 2061 47bb34b8ed8a78823eb0c886abfb9f4d ""
-  "sphinxoptionshyperref.sty" 1685303546 1094 79beb8b8a3f10784f8cce804e0f9d3aa ""
-  "sphinxpackageboxes.sty" 1685303546 36615 1d74c63e665ede6c648fa08c42ea70fb ""
-  "sphinxpackagefootnote.sty" 1685303546 15254 d93f70cf000a9adb198015bf1b2f136c ""
+  "/var/lib/texmf/web2c/pdftex/pdflatex.fmt" 1685506326 4791332 2906fb9114dfe18bf39728f7349fcfef ""
+  "esgemme.aux" 1686237775 6348 1244a872c7c4ec4cff5b0c77dffc5bc7 "pdflatex"
+  "esgemme.ind" 1686042164 0 d41d8cd98f00b204e9800998ecf8427e "makeindex esgemme.idx"
+  "esgemme.out" 1686237775 4671 f9636305672cbaa8157655b3e9e85a68 "pdflatex"
+  "esgemme.tex" 1686237774 18623 4ac2337e82ebd23f53589270d0e67939 ""
+  "esgemme.toc" 1686237775 1853 2379c1748ec7d176d556041991ae769a "pdflatex"
+  "sphinx.sty" 1686042164 44560 f9fbf51072c954d129c9bd5284cc4ccf ""
+  "sphinxhighlight.sty" 1686237774 7490 72d023191655734567e0798eade2a1f7 ""
+  "sphinxlatexadmonitions.sty" 1686042164 10989 c38302e64c2bb47779f086869b246760 ""
+  "sphinxlatexcontainers.sty" 1686042164 901 d3a3a1b7b2547f47ade2499350b5c420 ""
+  "sphinxlatexgraphics.sty" 1686042164 4840 a9578332b6f3b35e198751fb632c9b79 ""
+  "sphinxlatexindbibtoc.sty" 1686042164 2066 b93f8504d02f6337fde3074b179de55e ""
+  "sphinxlatexlists.sty" 1686042164 5139 c2de2a1d98d3c6ceedfe46505abd3c07 ""
+  "sphinxlatexliterals.sty" 1686042164 46048 2b66269d0ecf11768a14b5de4ddf9051 ""
+  "sphinxlatexnumfig.sty" 1686042164 4532 3633caf84afa1a98e1a060b7868202bb ""
+  "sphinxlatexobjects.sty" 1686042164 9067 1f9a0f04e0268b8abeb7d37165057523 ""
+  "sphinxlatexshadowbox.sty" 1686042164 5066 97a2be0d1dfdc98548b7461f1949b95f ""
+  "sphinxlatexstyleheadings.sty" 1686042164 3445 a1582a5f3b336dcffa71b5ca3d8fc31f ""
+  "sphinxlatexstylepage.sty" 1686042164 3064 abce6c3018a84afee0afb08a431944ea ""
+  "sphinxlatexstyletext.sty" 1686042164 8232 280fdc24a7889c35e545cd62e6cba921 ""
+  "sphinxlatextables.sty" 1686042164 57830 16f2773b765508003aec5d08680f39b9 ""
+  "sphinxmanual.cls" 1686042164 4241 7b0d7a37df7b5715fb0dbd585c52ecdb ""
+  "sphinxmessages.sty" 1686237774 745 3f5fcd6cdd7964ed608767954a8ced6f ""
+  "sphinxoptionsgeometry.sty" 1686042164 2061 47bb34b8ed8a78823eb0c886abfb9f4d ""
+  "sphinxoptionshyperref.sty" 1686042164 1094 79beb8b8a3f10784f8cce804e0f9d3aa ""
+  "sphinxpackageboxes.sty" 1686042164 36615 1d74c63e665ede6c648fa08c42ea70fb ""
+  "sphinxpackagefootnote.sty" 1686042164 15254 d93f70cf000a9adb198015bf1b2f136c ""
   (generated)
   "esgemme.toc"
+  "esgemme.pdf"
+  "esgemme.aux"
   "esgemme.log"
   "esgemme.idx"
   "esgemme.out"
-  "esgemme.pdf"
-  "esgemme.aux"

docs/_build/latex/esgemme.log

-This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex 2023.5.28)  30 MAY 2023 15:39
+This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex 2023.5.31)  8 JUN 2023 17:22
 entering extended mode
  restricted \write18 enabled.
  %&-line parsing enabled.
@@ -860,20 +860,14 @@ LaTeX Font Info:    Font shape `T1/txtt/b/n' in size <10> not available
 
 ]
 Chapter 2.
-
-Underfull \hbox (badness 10000) in paragraph at lines 270--274
-\T1/qtm/m/n/10 By de-fault, ES-GEMME will out-put the fol-low-ing files: * myPr
-ot_normPred_evolEpi.txt *
- []
-
-[5] [6
-
-]
+[5] [6]
 Chapter 3.
-[7] [8]
+[7
+
+] [8]
 Chapter 4.
 LaTeX Font Info:    Trying to load font information for TS1+qtm on input line 4
-05.
+74.
 (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
 File: ts1qtm.fd 2009/09/25 v1.2 font definition file for TS1/qtm
 ) [9
@@ -883,21 +877,21 @@ File: ts1qtm.fd 2009/09/25 v1.2 font definition file for TS1/qtm
 ]
 Chapter 5.
 (./esgemme.ind)
-Package atveryend Info: Empty hook `BeforeClearDocument' on input line 478.
+Package atveryend Info: Empty hook `BeforeClearDocument' on input line 547.
  [11]
-Package atveryend Info: Empty hook `AfterLastShipout' on input line 478.
+Package atveryend Info: Empty hook `AfterLastShipout' on input line 547.
  (./esgemme.aux)
-Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 478.
-Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 478.
+Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 547.
+Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 547.
 Package rerunfilecheck Info: File `esgemme.out' has not changed.
-(rerunfilecheck)             Checksum: 70B9B9C1AED09758E4D1AF545C6738B0;3604.
-Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 478.
+(rerunfilecheck)             Checksum: F9636305672CBAA8157655B3E9E85A68;4671.
+Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 547.
  ) 
 Here is how much of TeX's memory you used:
- 15093 strings out of 483183
- 228386 string characters out of 5966292
- 499469 words of memory out of 5000000
- 29683 multiletter control sequences out of 15000+600000
+ 15105 strings out of 483183
+ 228681 string characters out of 5966292
+ 499733 words of memory out of 5000000
+ 29689 multiletter control sequences out of 15000+600000
  580415 words of font info for 63 fonts, out of 8000000 for 9000
  15 hyphenation exceptions out of 8191
  38i,11n,51p,432b,613s stack positions out of 5000i,500n,10000p,200000b,80000s
@@ -909,10 +903,10 @@ e/texmf/fonts/type1/public/tex-gyre/qhvbi.pfb></usr/share/texmf/fonts/type1/pub
 lic/tex-gyre/qtmb.pfb></usr/share/texmf/fonts/type1/public/tex-gyre/qtmr.pfb></
 usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt.pfb></usr/share/
 texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb>
-Output written on esgemme.pdf (15 pages, 149485 bytes).
+Output written on esgemme.pdf (15 pages, 152415 bytes).
 PDF statistics:
- 223 PDF objects out of 1000 (max. 8388607)
- 191 compressed objects within 2 object streams
- 43 named destinations out of 1000 (max. 500000)
- 149 words of extra memory for PDF output out of 10000 (max. 10000000)
+ 243 PDF objects out of 1000 (max. 8388607)
+ 210 compressed objects within 3 object streams
+ 49 named destinations out of 1000 (max. 500000)
+ 173 words of extra memory for PDF output out of 10000 (max. 10000000)
 

docs/_build/latex/esgemme.out

@@ -6,11 +6,14 @@
 \BOOKMARK [2][-]{subsection.1.3.2}{\376\377\000P\000r\000e\000d\000i\000c\000t\000i\000n\000g\000\040\000t\000h\000e\000\040\000e\000f\000f\000e\000c\000t\000\040\000o\000f\000\040\000a\000\040\000s\000u\000b\000s\000e\000t\000\040\000o\000f\000\040\000s\000i\000n\000g\000l\000e\000\040\000p\000o\000i\000n\000t\000\040\000m\000u\000t\000a\000t\000i\000o\000n\000s}{section.1.3}% 6
 \BOOKMARK [1][-]{section.1.4}{\376\377\000M\000u\000l\000t\000i\000p\000l\000e\000\040\000p\000o\000i\000n\000t\000\040\000m\000u\000t\000a\000t\000i\000o\000n\000\040\000c\000a\000l\000c\000u\000l\000a\000t\000i\000o\000n\000s}{chapter.1}% 7
 \BOOKMARK [1][-]{section.1.5}{\376\377\000R\000u\000n\000n\000i\000n\000g\000\040\000s\000e\000v\000e\000r\000a\000l\000\040\000j\000o\000b\000s\000\040\000u\000s\000i\000n\000g\000\040\000d\000o\000c\000k\000e\000r}{chapter.1}% 8
-\BOOKMARK [0][-]{chapter.2}{\376\377\000A\000n\000a\000l\000y\000z\000i\000n\000g\000\040\000t\000h\000e\000\040\000E\000S\000G\000E\000M\000M\000E\000\040\000o\000u\000t\000p\000u\000t}{}% 9
-\BOOKMARK [0][-]{chapter.3}{\376\377\000P\000r\000e\000p\000a\000r\000i\000n\000g\000\040\000Y\000o\000u\000r\000\040\000O\000w\000n\000\040\000I\000n\000p\000u\000t}{}% 10
-\BOOKMARK [1][-]{section.3.1}{\376\377\000P\000r\000e\000p\000a\000r\000i\000n\000g\000\040\000Y\000o\000u\000r\000\040\000I\000n\000p\000u\000t\000\040\000M\000S\000A\000\040\000a\000n\000d\000\040\000P\000D\000B\000\040\000w\000i\000t\000h\000\040\000C\000o\000l\000a\000b\000f\000o\000l\000d}{chapter.3}% 11
-\BOOKMARK [0][-]{chapter.4}{\376\377\000I\000n\000s\000t\000a\000l\000l\000a\000t\000i\000o\000n}{}% 12
-\BOOKMARK [1][-]{section.4.1}{\376\377\000I\000n\000s\000t\000a\000l\000l\000i\000n\000g\000\040\000t\000h\000e\000\040\000d\000e\000p\000e\000n\000d\000e\000n\000c\000i\000e\000s\000:}{chapter.4}% 13
-\BOOKMARK [1][-]{section.4.2}{\376\377\000G\000e\000t\000t\000i\000n\000g\000\040\000t\000h\000e\000\040\000s\000o\000u\000r\000c\000e\000\040\000c\000o\000d\000e\000\040\000a\000n\000d\000\040\000p\000r\000e\000p\000a\000r\000i\000n\000g\000\040\000t\000h\000e\000\040\000e\000n\000v\000i\000r\000o\000n\000m\000e\000n\000t\000:}{chapter.4}% 14
-\BOOKMARK [1][-]{section.4.3}{\376\377\000C\000o\000n\000f\000i\000g\000u\000r\000i\000n\000g\000\040\000d\000e\000f\000a\000u\000l\000t\000.\000c\000o\000n\000f\000\040\000f\000i\000l\000e}{chapter.4}% 15
-\BOOKMARK [0][-]{chapter.5}{\376\377\000I\000n\000d\000i\000c\000e\000s\000\040\000a\000n\000d\000\040\000t\000a\000b\000l\000e\000s}{}% 16
+\BOOKMARK [0][-]{chapter.2}{\376\377\000A\000n\000a\000l\000y\000z\000i\000n\000g\000\040\000a\000n\000d\000\040\000M\000o\000d\000i\000f\000y\000i\000n\000g\000\040\000t\000h\000e\000\040\000E\000S\000G\000E\000M\000M\000E\000\040\000O\000u\000t\000p\000u\000t}{}% 9
+\BOOKMARK [1][-]{section.2.1}{\376\377\000R\000a\000w\000\040\000E\000S\000G\000E\000M\000M\000E\000\040\000S\000c\000o\000r\000e\000s\000\040\000a\000n\000d\000\040\000T\000h\000e\000i\000r\000\040\000I\000n\000t\000e\000r\000p\000r\000e\000t\000a\000t\000i\000o\000n}{chapter.2}% 10
+\BOOKMARK [1][-]{section.2.2}{\376\377\000E\000n\000t\000i\000r\000e\000\040\000S\000i\000n\000g\000l\000e\000\040\000P\000o\000i\000n\000t\000\040\000M\000u\000t\000a\000t\000i\000o\000n\000\040\000L\000a\000n\000d\000s\000c\000a\000p\000e\000\040\000C\000a\000l\000c\000u\000l\000a\000t\000i\000o\000n\000s}{chapter.2}% 11
+\BOOKMARK [1][-]{section.2.3}{\376\377\000S\000e\000l\000e\000c\000t\000e\000d\000\040\000S\000i\000n\000g\000l\000e\000\040\000P\000o\000i\000n\000t\000\040\000o\000r\000\040\000M\000u\000l\000t\000i\000p\000l\000e\000\040\000P\000o\000i\000n\000t\000\040\000M\000u\000t\000a\000t\000i\000o\000n\000\040\000C\000a\000l\000c\000u\000l\000a\000t\000i\000o\000n\000s}{chapter.2}% 12
+\BOOKMARK [0][-]{chapter.3}{\376\377\000P\000r\000e\000p\000a\000r\000i\000n\000g\000\040\000Y\000o\000u\000r\000\040\000O\000w\000n\000\040\000I\000n\000p\000u\000t}{}% 13
+\BOOKMARK [1][-]{section.3.1}{\376\377\000P\000r\000e\000p\000a\000r\000i\000n\000g\000\040\000Y\000o\000u\000r\000\040\000I\000n\000p\000u\000t\000\040\000M\000S\000A\000\040\000a\000n\000d\000\040\000P\000D\000B\000\040\000w\000i\000t\000h\000\040\000C\000o\000l\000a\000b\000f\000o\000l\000d}{chapter.3}% 14
+\BOOKMARK [0][-]{chapter.4}{\376\377\000I\000n\000s\000t\000a\000l\000l\000a\000t\000i\000o\000n}{}% 15
+\BOOKMARK [1][-]{section.4.1}{\376\377\000I\000n\000s\000t\000a\000l\000l\000i\000n\000g\000\040\000t\000h\000e\000\040\000d\000e\000p\000e\000n\000d\000e\000n\000c\000i\000e\000s\000:}{chapter.4}% 16
+\BOOKMARK [1][-]{section.4.2}{\376\377\000G\000e\000t\000t\000i\000n\000g\000\040\000t\000h\000e\000\040\000s\000o\000u\000r\000c\000e\000\040\000c\000o\000d\000e\000\040\000a\000n\000d\000\040\000p\000r\000e\000p\000a\000r\000i\000n\000g\000\040\000t\000h\000e\000\040\000e\000n\000v\000i\000r\000o\000n\000m\000e\000n\000t\000:}{chapter.4}% 17
+\BOOKMARK [1][-]{section.4.3}{\376\377\000C\000o\000n\000f\000i\000g\000u\000r\000i\000n\000g\000\040\000d\000e\000f\000a\000u\000l\000t\000.\000c\000o\000n\000f\000\040\000f\000i\000l\000e}{chapter.4}% 18
+\BOOKMARK [0][-]{chapter.5}{\376\377\000I\000n\000d\000i\000c\000e\000s\000\040\000a\000n\000d\000\040\000t\000a\000b\000l\000e\000s}{}% 19

docs/_build/latex/esgemme.tex

@@ -64,7 +64,7 @@
 
 
 \title{esgemme}
-\date{May 30, 2023}
+\date{Jun 08, 2023}
 \release{1.3.0}
 \author{Mustafa Tekpinar}
 \newcommand{\sphinxlogo}{\vbox{}}
@@ -265,21 +265,90 @@ mutation and its predicted effect, separated by a space.
 \sphinxstepscope
 
 
-\chapter{Analyzing the ESGEMME output}
-\label{\detokenize{analysis:analyzing-the-esgemme-output}}\label{\detokenize{analysis::doc}}
+\chapter{Analyzing and Modifying the ESGEMME Output}
+\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
-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
-query sequence. If the user provides her/his own list of mutations, then
-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
-the normalized predicted effects.
+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.
+\end{quote}
+
+\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
 

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}%

docs/analysis.rst

-Analyzing the ESGEMME output
-----------------------------
-
-By default, ESGEMME will output the following files: \*
-myProt_normPred_evolEpi.txt \* myProt_normPred_evolInd.txt \*
-myProt_normPred_evolCombi.txt
-
-The most important output file is **myProt_normPred_evolCombi.txt**. The
-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
-query sequence. If the user provides her/his own list of mutations, then
-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
-the normalized predicted effects.
+Analyzing and Modifying the ESGEMME Output
+==========================================
+
+Raw ESGEMME Scores and Their Interpretation
+-------------------------------------------
+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, 
+while values close to 0 means the mutation does not have any significant impact.
+
+We should note that most of the 'impactful' mutations are deleterious but 
+it is not always the case. 
+
+Entire Single Point Mutation Landscape Calculations
+---------------------------------------------------
+
+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
+
+
+
+

computePred.R → esgemme/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
-blosum62p = as.matrix(read.table(paste0(Sys.getenv("ESGEMME_PATH"),"/data/blosum62p.txt"),row.names=1))
-bgp = blosum62p[order(rownames(blosum62p)),order(colnames(blosum62p))]
-bg = apply(bgp,1,sum)
+# # BLOSUM62  matrix
+# blosum62p = as.matrix(read.table(paste0(Sys.getenv("ESGEMME_PATH"),"/data/blosum62p.txt"),row.names=1))
+# bgp = blosum62p[order(rownames(blosum62p)),order(colnames(blosum62p))]
+# bg = apply(bgp,1,sum)
 
 # get arguemnts 
 args = commandArgs(trailingOnly = TRUE)

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"):
-       os.remove("default.conf")
+    if os.path.isfile("default.conf"):
+        os.remove("default.conf")
 
     if verbosity == False:
         if os.path.isfile(prot+"_normPred_evolInd.txt"):

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
 

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']},
       )