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PRESCOTT
Commit 4ff99431 by Mustafa Tekpinar
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Documentation update.

parent 56d41188
Showing with 25 additions and 23 deletions
README.md
......@@ -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.
docs/_build/html/installation.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="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/>
......
docs/_build/html/introduction.html
......@@ -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>
......
docs/_build/latex/prescott.fdb_latexmk
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"prescott.idx" 1703579054 0 d41d8cd98f00b204e9800998ecf8427e "pdflatex"
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......@@ -140,13 +140,13 @@
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......@@ -161,7 +161,7 @@
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......
docs/_build/latex/prescott.log
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.8.21) 30 NOV 2023 14:59
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.8.21) 26 DEC 2023 09:24
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
......@@ -835,7 +835,7 @@ Package rerunfilecheck Info: File `prescott.out' has not changed.
Here is how much of TeX's memory you used:
14699 strings out of 480204
234164 string characters out of 5895010
598549 words of memory out of 5000000
599549 words of memory out of 5000000
32215 multiletter control sequences out of 15000+600000
520869 words of font info for 70 fonts, out of 8000000 for 9000
37 hyphenation exceptions out of 8191
......@@ -850,7 +850,7 @@ usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt.pfb></usr/share/
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ts/type1/public/txfonts/tcxtt.pfb>
Output written on prescott.pdf (23 pages, 177499 bytes).
Output written on prescott.pdf (23 pages, 177507 bytes).
PDF statistics:
350 PDF objects out of 1000 (max. 8388607)
304 compressed objects within 4 object streams
......
docs/_build/latex/prescott.tex
......@@ -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.
\sphinxstepscope
......
docs/introduction.rst
......@@ -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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