Skip to content

P
PRESCOTT
Commit 4ff99431 by Mustafa Tekpinar
Options

Documentation update.

parent 56d41188
Showing with 25 additions and 23 deletions
README.md
...@@ -24,7 +24,7 @@ escott requires two files: ...@@ -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: 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 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. For testing purpose, you can find some example input files for BLAT protein in data/ folder of this repository.
### Input Data Requirements for prescott ### 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 ...@@ -76,5 +76,5 @@ PRESCOTT is implemented in Python 3 and R. It has been tested only on Linux. Sin
# Cite # 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 @@ ...@@ -19,7 +19,7 @@
<script src="_static/js/theme.js"></script> <script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" /> <link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.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> </head>
<body class="wy-body-for-nav"> <body class="wy-body-for-nav">
...@@ -47,6 +47,7 @@ ...@@ -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="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="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="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-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="#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> <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 ...@@ -231,7 +232,7 @@ rm -rf master.zip plmc-master
</div> </div>
</div> </div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer"> <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> </div>
<hr/> <hr/>
......
docs/_build/html/introduction.html
...@@ -63,6 +63,7 @@ ...@@ -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="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="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="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> <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
</ul> </ul>
...@@ -122,7 +123,7 @@ run colabfold: ...@@ -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> <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 <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 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> 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 <p>For testing purpose, you can find some example input files for BLAT
protein in data/ folder of this repository.</p> protein in data/ folder of this repository.</p>
...@@ -195,7 +196,7 @@ in the docs folder of this repository):</p> ...@@ -195,7 +196,7 @@ in the docs folder of this repository):</p>
</section> </section>
<section id="citation"> <section id="citation">
<h2>Citation<a class="headerlink" href="#citation" title="Permalink to this heading"></a></h2> <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>
</section> </section>
......
docs/_build/latex/prescott.fdb_latexmk
# Fdb version 3 # Fdb version 3
["makeindex prescott.idx"] 1691770116 "prescott.idx" "prescott.ind" "prescott" 1701352785 ["makeindex prescott.idx"] 1691770116 "prescott.idx" "prescott.ind" "prescott" 1703579054
"prescott.idx" 1701352785 0 d41d8cd98f00b204e9800998ecf8427e "pdflatex" "prescott.idx" 1703579054 0 d41d8cd98f00b204e9800998ecf8427e "pdflatex"
(generated) (generated)
"prescott.ilg" "prescott.ilg"
"prescott.ind" "prescott.ind"
["pdflatex"] 1701352784 "prescott.tex" "prescott.pdf" "prescott" 1701352785 ["pdflatex"] 1703579053 "prescott.tex" "prescott.pdf" "prescott" 1703579054
"/etc/texmf/web2c/texmf.cnf" 1686915816 475 c0e671620eb5563b2130f56340a5fde8 "" "/etc/texmf/web2c/texmf.cnf" 1686915816 475 c0e671620eb5563b2130f56340a5fde8 ""
"/usr/share/texlive/texmf-dist/fonts/map/fontname/texfonts.map" 1577235249 3524 cb3e574dea2d1052e39280babc910dc8 "" "/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 "" "/usr/share/texlive/texmf-dist/fonts/tfm/jknappen/ec/ecrm1000.tfm" 1136768653 3584 adb004a0c8e7c46ee66cad73671f37b4 ""
...@@ -140,13 +140,13 @@ ...@@ -140,13 +140,13 @@
"/usr/share/texmf/web2c/texmf.cnf" 1644012257 39432 7155514e09a3d69036fac785183a21c2 "" "/usr/share/texmf/web2c/texmf.cnf" 1644012257 39432 7155514e09a3d69036fac785183a21c2 ""
"/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map" 1692610720 128028 f533b797fba58d231669ea19e894e23e "" "/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map" 1692610720 128028 f533b797fba58d231669ea19e894e23e ""
"/var/lib/texmf/web2c/pdftex/pdflatex.fmt" 1692610730 1455466 cf5d347cc06e6f91065ccb2619b82e95 "" "/var/lib/texmf/web2c/pdftex/pdflatex.fmt" 1692610730 1455466 cf5d347cc06e6f91065ccb2619b82e95 ""
"prescott.aux" 1701352785 9143 aed8bca5ac12c0ebd50681d413e58d41 "pdflatex" "prescott.aux" 1703579054 9143 aed8bca5ac12c0ebd50681d413e58d41 "pdflatex"
"prescott.ind" 1694694190 0 d41d8cd98f00b204e9800998ecf8427e "makeindex prescott.idx" "prescott.ind" 1694694190 0 d41d8cd98f00b204e9800998ecf8427e "makeindex prescott.idx"
"prescott.out" 1701352785 6500 451b70ed444684f0bdee8ace15638a1b "pdflatex" "prescott.out" 1703579054 6500 451b70ed444684f0bdee8ace15638a1b "pdflatex"
"prescott.tex" 1701352784 36391 7990fd9a7dcbf4423b4d9f0a3d541afe "" "prescott.tex" 1703579053 36406 2f8f00d2455f5aa83552bb6ff02b36b6 ""
"prescott.toc" 1701352785 2791 ec37ce19b28894e4de4791b16a96dddb "pdflatex" "prescott.toc" 1703579054 2791 ec37ce19b28894e4de4791b16a96dddb "pdflatex"
"sphinx.sty" 1691571542 12780 919e6ba449302e2597e7722681a087c6 "" "sphinx.sty" 1691571542 12780 919e6ba449302e2597e7722681a087c6 ""
"sphinxhighlight.sty" 1701352784 6679 76d10c62e0f0661410b46f5db6118e26 "" "sphinxhighlight.sty" 1703579053 6679 76d10c62e0f0661410b46f5db6118e26 ""
"sphinxlatexadmonitions.sty" 1691571543 6238 2d867d769abf3f72abc17ef52adff78b "" "sphinxlatexadmonitions.sty" 1691571543 6238 2d867d769abf3f72abc17ef52adff78b ""
"sphinxlatexcontainers.sty" 1691571543 901 d3a3a1b7b2547f47ade2499350b5c420 "" "sphinxlatexcontainers.sty" 1691571543 901 d3a3a1b7b2547f47ade2499350b5c420 ""
"sphinxlatexgraphics.sty" 1691571543 4840 a9578332b6f3b35e198751fb632c9b79 "" "sphinxlatexgraphics.sty" 1691571543 4840 a9578332b6f3b35e198751fb632c9b79 ""
...@@ -161,7 +161,7 @@ ...@@ -161,7 +161,7 @@
"sphinxlatexstyletext.sty" 1691571543 6177 c18841ce3fafc366cd3b145f8faa4c37 "" "sphinxlatexstyletext.sty" 1691571543 6177 c18841ce3fafc366cd3b145f8faa4c37 ""
"sphinxlatextables.sty" 1691571542 21848 2827eb0b11b99b185a8b77317d3e131c "" "sphinxlatextables.sty" 1691571542 21848 2827eb0b11b99b185a8b77317d3e131c ""
"sphinxmanual.cls" 1691571543 4241 7b0d7a37df7b5715fb0dbd585c52ecdb "" "sphinxmanual.cls" 1691571543 4241 7b0d7a37df7b5715fb0dbd585c52ecdb ""
"sphinxmessages.sty" 1701352784 745 3f5fcd6cdd7964ed608767954a8ced6f "" "sphinxmessages.sty" 1703579053 745 3f5fcd6cdd7964ed608767954a8ced6f ""
"sphinxoptionsgeometry.sty" 1691571542 2061 47bb34b8ed8a78823eb0c886abfb9f4d "" "sphinxoptionsgeometry.sty" 1691571542 2061 47bb34b8ed8a78823eb0c886abfb9f4d ""
"sphinxoptionshyperref.sty" 1691571543 1094 79beb8b8a3f10784f8cce804e0f9d3aa "" "sphinxoptionshyperref.sty" 1691571543 1094 79beb8b8a3f10784f8cce804e0f9d3aa ""
"sphinxpackagefootnote.sty" 1691571543 15217 dd26fe418b6fb1b26b18f042a7f43d40 "" "sphinxpackagefootnote.sty" 1691571543 15217 dd26fe418b6fb1b26b18f042a7f43d40 ""
......
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 entering extended mode
restricted \write18 enabled. restricted \write18 enabled.
%&-line parsing enabled. %&-line parsing enabled.
...@@ -835,7 +835,7 @@ Package rerunfilecheck Info: File `prescott.out' has not changed. ...@@ -835,7 +835,7 @@ Package rerunfilecheck Info: File `prescott.out' has not changed.
Here is how much of TeX's memory you used: Here is how much of TeX's memory you used:
14699 strings out of 480204 14699 strings out of 480204
234164 string characters out of 5895010 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 32215 multiletter control sequences out of 15000+600000
520869 words of font info for 70 fonts, out of 8000000 for 9000 520869 words of font info for 70 fonts, out of 8000000 for 9000
37 hyphenation exceptions out of 8191 37 hyphenation exceptions out of 8191
...@@ -850,7 +850,7 @@ usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt.pfb></usr/share/ ...@@ -850,7 +850,7 @@ usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt.pfb></usr/share/
texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/tex texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/texmf-dist/fon mf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/txfonts/tcxtt.pfb> 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: PDF statistics:
350 PDF objects out of 1000 (max. 8388607) 350 PDF objects out of 1000 (max. 8388607)
304 compressed objects within 4 object streams 304 compressed objects within 4 object streams
......
docs/_build/latex/prescott.tex
...@@ -61,7 +61,7 @@ ...@@ -61,7 +61,7 @@
\title{prescott} \title{prescott}
\date{Nov 30, 2023} \date{Dec 26, 2023}
\release{1.6.0} \release{1.6.0}
\author{Mustafa Tekpinar} \author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}} \newcommand{\sphinxlogo}{\vbox{}}
...@@ -136,7 +136,7 @@ run colabfold: ...@@ -136,7 +136,7 @@ run colabfold:
\sphinxAtStartPar \sphinxAtStartPar
Please note that the MSA file produced by colabfold (a3m file) can 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 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/}). such as ugene (\sphinxurl{http://ugene.net/}) or jalview (\sphinxurl{https://www.jalview.org/}).
\sphinxAtStartPar \sphinxAtStartPar
...@@ -256,7 +256,7 @@ in the docs folder of this repository): ...@@ -256,7 +256,7 @@ in the docs folder of this repository):
\section{Citation} \section{Citation}
\label{\detokenize{introduction:citation}} \label{\detokenize{introduction:citation}}
\sphinxAtStartPar \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 \sphinxstepscope
......
docs/introduction.rst
...@@ -36,7 +36,7 @@ https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold ...@@ -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 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 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/). such as ugene (http://ugene.net/) or jalview (https://www.jalview.org/).
For testing purpose, you can find some example input files for BLAT For testing purpose, you can find some example input files for BLAT
...@@ -129,7 +129,7 @@ in the docs folder of this repository): ...@@ -129,7 +129,7 @@ in the docs folder of this repository):
Citation 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 .. |License: MIT| image:: https://img.shields.io/badge/License-MIT-yellow.svg
:target: https://opensource.org/licenses/MIT :target: https://opensource.org/licenses/MIT
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment