Commit 4ff99431 by Mustafa Tekpinar

Documentation update.

parent 56d41188
......@@ -24,7 +24,7 @@ escott 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 PRESCOTT. 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 programs that have a GUI, such as ugene (http://ugene.net/) or jalview (https://www.jalview.org/).
For testing purpose, you can find some example input files for BLAT protein in data/ folder of this repository.
### Input Data Requirements for prescott
......@@ -76,5 +76,5 @@ PRESCOTT is implemented in Python 3 and R. It has been tested only on Linux. Sin
# Cite
Mustafa Tekpinar, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
Mustafa Tekpinar, Laurent David, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
......@@ -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="prev" title="Preparing Your Own Input" href="input-preparation.html" />
<link rel="prev" title="Using ESCOTT via Singularity" href="singularity.html" />
</head>
<body class="wy-body-for-nav">
......@@ -47,6 +47,7 @@
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT 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="singularity.html">Using ESCOTT via Singularity</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-prescott">Preparation of the environment and installation of PRESCOTT</a></li>
......@@ -231,7 +232,7 @@ rm -rf master.zip plmc-master
</div>
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
<a href="input-preparation.html" class="btn btn-neutral float-left" title="Preparing Your Own Input" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
<a href="singularity.html" class="btn btn-neutral float-left" title="Using ESCOTT via Singularity" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
</div>
<hr/>
......
......@@ -63,6 +63,7 @@
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT 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="singularity.html">Using ESCOTT via Singularity</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
</ul>
......@@ -122,7 +123,7 @@ run colabfold:
<a class="reference external" href="https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb">https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb</a></p>
<p>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,
it in PRESCOTT. You can remove the gaps with programs that have a GUI,
such as ugene (<a class="reference external" href="http://ugene.net/">http://ugene.net/</a>) or jalview (<a class="reference external" href="https://www.jalview.org/">https://www.jalview.org/</a>).</p>
<p>For testing purpose, you can find some example input files for BLAT
protein in data/ folder of this repository.</p>
......@@ -195,7 +196,7 @@ in the docs folder of this repository):</p>
</section>
<section id="citation">
<h2>Citation<a class="headerlink" href="#citation" title="Permalink to this heading"></a></h2>
<p>Mustafa Tekpinar, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.</p>
<p>Mustafa Tekpinar, Laurent David, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.</p>
</section>
</section>
......
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# Fdb version 3
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Output written on prescott.pdf (23 pages, 177499 bytes).
Output written on prescott.pdf (23 pages, 177507 bytes).
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......@@ -61,7 +61,7 @@
\title{prescott}
\date{Nov 30, 2023}
\date{Dec 26, 2023}
\release{1.6.0}
\author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}}
......@@ -136,7 +136,7 @@ run colabfold:
\sphinxAtStartPar
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,
it in PRESCOTT. You can remove the gaps with programs that have a GUI,
such as ugene (\sphinxurl{http://ugene.net/}) or jalview (\sphinxurl{https://www.jalview.org/}).
\sphinxAtStartPar
......@@ -256,7 +256,7 @@ in the docs folder of this repository):
\section{Citation}
\label{\detokenize{introduction:citation}}
\sphinxAtStartPar
Mustafa Tekpinar, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
Mustafa Tekpinar, Laurent David, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
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......@@ -36,7 +36,7 @@ https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold
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,
it in PRESCOTT. You can remove the gaps with programs that have a GUI,
such as ugene (http://ugene.net/) or jalview (https://www.jalview.org/).
For testing purpose, you can find some example input files for BLAT
......@@ -129,7 +129,7 @@ in the docs folder of this repository):
Citation
--------
Mustafa Tekpinar, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
Mustafa Tekpinar, Laurent David, Thomas Henry, Alessandra Carbone. PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect.
.. |License: MIT| image:: https://img.shields.io/badge/License-MIT-yellow.svg
:target: https://opensource.org/licenses/MIT
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