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PRESCOTT
Commit 6dbd9c68 by Mustafa Tekpinar
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Simplified escott UI by removing args.fastaFile requirement.

parent e6123f25
Showing with 53 additions and 45 deletions
README.md
......@@ -43,7 +43,7 @@ Let's assume that our input MSA is inputAli.fasta and input.pdb is our structure
Run the program by issuing the following command in a bash terminal:
```bash
escott inputAli.fasta -f inputAli.fasta --pdbfile input.pdb
escott inputAli.fasta --pdbfile input.pdb
```
A quick help can be accessed by typing
......
docs/_build/html/_sources/docker.rst.txt
......@@ -81,7 +81,7 @@ In this step, we will use only evolutionary information from an MSA file:
.. code:: bash
escott aliBLAT.fasta -f aliBLAT.fasta
escott aliBLAT.fasta
After a few minutes of calculation, you must see at least two files named
BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
......@@ -93,7 +93,7 @@ evolutionary information:
.. code:: bash
escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
escott aliBLAT.fasta --pdbfile blat-af2.pdb
Predicting the effect of a subset of single point mutations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
......@@ -111,13 +111,13 @@ structural information. First, let's do it without structural information:
.. code:: bash
escott aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
escott aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way:
.. code:: bash
escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb \
escott aliBLAT.fasta --pdbfile blat-af2.pdb \
-m Stiffler_2015_BLAT_ECOLX.mut
You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output
......
docs/_build/html/docker.html
......@@ -19,8 +19,8 @@
<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 and Modifying the PRESCOTT Output" href="analysis.html" />
<link rel="prev" title="Welcome to esgemme’s documentation!" href="index.html" />
<link rel="next" title="Analyzing and Modifying the ESCOTT Output" href="analysis.html" />
<link rel="prev" title="Introduction" href="introduction.html" />
</head>
<body class="wy-body-for-nav">
......@@ -44,6 +44,7 @@
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Using ESCOTT via Docker</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#requirements">Requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="#getting-the-example-input-data">Getting the example input data</a></li>
......@@ -56,7 +57,7 @@
<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 and Modifying the PRESCOTT 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="installation.html">Installation</a></li>
</ul>
......@@ -144,7 +145,7 @@ docker container are pointing to the same place.</p>
<section id="obtaining-the-entire-single-point-mutation-landscape">
<h3>Obtaining the entire single point mutation landscape<a class="headerlink" href="#obtaining-the-entire-single-point-mutation-landscape" title="Permalink to this heading"></a></h3>
<p>In this step, we will use only evolutionary information from an MSA file:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott aliBLAT.fasta -f aliBLAT.fasta
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott aliBLAT.fasta
</pre></div>
</div>
<p>After a few minutes of calculation, you must see at least two files named
......@@ -153,7 +154,7 @@ the entire single point mutational landscape of BLAT protein in these
files.</p>
<p>If you want to utilize structural information (highly recommended) as well as
evolutionary information:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott aliBLAT.fasta --pdbfile blat-af2.pdb
</pre></div>
</div>
</section>
......@@ -168,11 +169,11 @@ Fortunately, we have an example mut in data folder of PRESCOTT repository.</p>
</div>
<p>Similar to the previous step, there are two possible ways to do the calculations: with or without
structural information. First, let’s do it without structural information:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
</pre></div>
</div>
<p>You can include structural information in the following way:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb <span class="se">\</span>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott aliBLAT.fasta --pdbfile blat-af2.pdb <span class="se">\</span>
-m Stiffler_2015_BLAT_ECOLX.mut
</pre></div>
</div>
......@@ -206,8 +207,8 @@ mutation and its predicted effect, separated by a space.</p>
</div>
</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 and Modifying the PRESCOTT Output" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
<a href="introduction.html" class="btn btn-neutral float-left" title="Introduction" 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 and Modifying the ESCOTT Output" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
</div>
<hr/>
......
docs/_build/html/introduction.html
......@@ -149,7 +149,7 @@ documentation for further details.</p>
<p>Let’s assume that our input MSA is inputAli.fasta and input.pdb is our
structure file in PDB format.</p>
<p>Run the program by issuing the following command in a bash terminal:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott inputAli.fasta -f inputAli.fasta --pdbfile input.pdb
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>escott inputAli.fasta --pdbfile input.pdb
</pre></div>
</div>
<p>A quick help can be accessed by typing</p>
......
docs/_build/latex/prescott.fdb_latexmk
# Fdb version 3
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"prescott.idx" 1696926737 0 d41d8cd98f00b204e9800998ecf8427e "pdflatex"
["makeindex prescott.idx"] 1691770116 "prescott.idx" "prescott.ind" "prescott" 1696952313
"prescott.idx" 1696952313 0 d41d8cd98f00b204e9800998ecf8427e "pdflatex"
(generated)
"prescott.ilg"
"prescott.ind"
["pdflatex"] 1696926736 "prescott.tex" "prescott.pdf" "prescott" 1696926737
["pdflatex"] 1696952313 "prescott.tex" "prescott.pdf" "prescott" 1696952313
"/etc/texmf/web2c/texmf.cnf" 1686915816 475 c0e671620eb5563b2130f56340a5fde8 ""
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"/usr/share/texlive/texmf-dist/fonts/tfm/jknappen/ec/ecrm1000.tfm" 1136768653 3584 adb004a0c8e7c46ee66cad73671f37b4 ""
......@@ -140,13 +140,13 @@
"/usr/share/texmf/web2c/texmf.cnf" 1644012257 39432 7155514e09a3d69036fac785183a21c2 ""
"/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map" 1692610720 128028 f533b797fba58d231669ea19e894e23e ""
"/var/lib/texmf/web2c/pdftex/pdflatex.fmt" 1692610730 1455466 cf5d347cc06e6f91065ccb2619b82e95 ""
"prescott.aux" 1696926737 8757 49bd9be15e4a1990a75c401ccac48f11 "pdflatex"
"prescott.aux" 1696952313 8757 49bd9be15e4a1990a75c401ccac48f11 "pdflatex"
"prescott.ind" 1694694190 0 d41d8cd98f00b204e9800998ecf8427e "makeindex prescott.idx"
"prescott.out" 1696926737 6307 8119393c8f110ffbb217a1e7b2c390de "pdflatex"
"prescott.tex" 1696926736 31550 20f37acb31b6833dc824f7480aecb279 ""
"prescott.toc" 1696926737 2706 6a2a8c488f73b27e9fedb6cddefdfa53 "pdflatex"
"prescott.out" 1696952313 6307 8119393c8f110ffbb217a1e7b2c390de "pdflatex"
"prescott.tex" 1696952313 31424 e9a6a4fd7d4a4a47e172ef1aaef86828 ""
"prescott.toc" 1696952313 2706 6a2a8c488f73b27e9fedb6cddefdfa53 "pdflatex"
"sphinx.sty" 1691571542 12780 919e6ba449302e2597e7722681a087c6 ""
"sphinxhighlight.sty" 1696926736 6679 76d10c62e0f0661410b46f5db6118e26 ""
"sphinxhighlight.sty" 1696952312 6679 76d10c62e0f0661410b46f5db6118e26 ""
"sphinxlatexadmonitions.sty" 1691571543 6238 2d867d769abf3f72abc17ef52adff78b ""
"sphinxlatexcontainers.sty" 1691571543 901 d3a3a1b7b2547f47ade2499350b5c420 ""
"sphinxlatexgraphics.sty" 1691571543 4840 a9578332b6f3b35e198751fb632c9b79 ""
......@@ -161,7 +161,7 @@
"sphinxlatexstyletext.sty" 1691571543 6177 c18841ce3fafc366cd3b145f8faa4c37 ""
"sphinxlatextables.sty" 1691571542 21848 2827eb0b11b99b185a8b77317d3e131c ""
"sphinxmanual.cls" 1691571543 4241 7b0d7a37df7b5715fb0dbd585c52ecdb ""
"sphinxmessages.sty" 1696926736 745 3f5fcd6cdd7964ed608767954a8ced6f ""
"sphinxmessages.sty" 1696952313 745 3f5fcd6cdd7964ed608767954a8ced6f ""
"sphinxoptionsgeometry.sty" 1691571542 2061 47bb34b8ed8a78823eb0c886abfb9f4d ""
"sphinxoptionshyperref.sty" 1691571543 1094 79beb8b8a3f10784f8cce804e0f9d3aa ""
"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) 10 OCT 2023 10:32
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.8.21) 10 OCT 2023 17:38
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
......@@ -853,7 +853,7 @@ 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
mf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/txfonts/tcxtt.pfb>
Output written on prescott.pdf (21 pages, 172572 bytes).
Output written on prescott.pdf (21 pages, 172555 bytes).
PDF statistics:
329 PDF objects out of 1000 (max. 8388607)
286 compressed objects within 3 object streams
......
docs/_build/latex/prescott.tex
......@@ -185,7 +185,7 @@ structure file in PDB format.
Run the program by issuing the following command in a bash terminal:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
escott inputAli.fasta \PYGZhy{}f inputAli.fasta \PYGZhy{}\PYGZhy{}pdbfile input.pdb
escott inputAli.fasta \PYGZhy{}\PYGZhy{}pdbfile input.pdb
\end{sphinxVerbatim}
\sphinxAtStartPar
......@@ -342,7 +342,7 @@ docker container are pointing to the same place.
In this step, we will use only evolutionary information from an MSA file:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
escott aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta
escott aliBLAT.fasta
\end{sphinxVerbatim}
\sphinxAtStartPar
......@@ -356,7 +356,7 @@ If you want to utilize structural information (highly recommended) as well as
evolutionary information:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
escott aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta \PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb
escott aliBLAT.fasta \PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb
\end{sphinxVerbatim}
......@@ -377,14 +377,14 @@ Similar to the previous step, there are two possible ways to do the calculations
structural information. First, let’s do it without structural information:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
escott aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta \PYGZhy{}m Stiffler\PYGZus{}2015\PYGZus{}BLAT\PYGZus{}ECOLX.mut
escott aliBLAT.fasta \PYGZhy{}m Stiffler\PYGZus{}2015\PYGZus{}BLAT\PYGZus{}ECOLX.mut
\end{sphinxVerbatim}
\sphinxAtStartPar
You can include structural information in the following way:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
escott aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta \PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb \PYG{l+s+se}{\PYGZbs{}}
escott aliBLAT.fasta \PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb \PYG{l+s+se}{\PYGZbs{}}
\PYGZhy{}m Stiffler\PYGZus{}2015\PYGZus{}BLAT\PYGZus{}ECOLX.mut
\end{sphinxVerbatim}
......
docs/docker.rst
......@@ -81,7 +81,7 @@ In this step, we will use only evolutionary information from an MSA file:
.. code:: bash
escott aliBLAT.fasta -f aliBLAT.fasta
escott aliBLAT.fasta
After a few minutes of calculation, you must see at least two files named
BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
......@@ -93,7 +93,7 @@ evolutionary information:
.. code:: bash
escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
escott aliBLAT.fasta --pdbfile blat-af2.pdb
Predicting the effect of a subset of single point mutations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
......@@ -111,13 +111,13 @@ structural information. First, let's do it without structural information:
.. code:: bash
escott aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
escott aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way:
.. code:: bash
escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb \
escott aliBLAT.fasta --pdbfile blat-af2.pdb \
-m Stiffler_2015_BLAT_ECOLX.mut
You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output
......
docs/introduction.rst
......@@ -72,7 +72,7 @@ Run the program by issuing the following command in a bash terminal:
.. code:: bash
escott inputAli.fasta -f inputAli.fasta --pdbfile input.pdb
escott inputAli.fasta --pdbfile input.pdb
A quick help can be accessed by typing
......
examples/example-escott-script.sh
......@@ -20,7 +20,7 @@ then
echo "Running PRESCOTT with a user-provided alignment file."
echo "Using a previously produced prot_jet.res file to check reproducibility!"
escott ../data/aliBLAT.fasta -f ../data/aliBLAT.fasta --jetfile ../data/BLAT_jet.res
escott ../data/aliBLAT.fasta --jetfile ../data/BLAT_jet.res
elif [ "$1" == "withpdb" ]
then
......@@ -28,8 +28,7 @@ then
#Please note that CV isa structural feature and it can not be calculated if you don't specify a pdb file.
echo "Using blat-af2.pdb for the structural feature calculations!"
echo "Entire mutational map of the protein will be calculated!"
escott ../data/aliBLAT.fasta -f ../data/aliBLAT.fasta \
--pdbfile ../data/blat-af2.pdb
escott ../data/aliBLAT.fasta --pdbfile ../data/blat-af2.pdb
elif [ "$1" == "withpdb-withmutfile" ]
then
......@@ -37,13 +36,12 @@ then
#Please note that CV isa structural feature and it can not be calculated if you don't specify a pdb file.
echo "Using blat-af2.pdb for the structural feature calculations!"
echo "Only effects of mutations specified in the Stiffler_2015_BLAT_ECOLX.mut file will be calculated!"
escott ../data/aliBLAT.fasta -f ../data/aliBLAT.fasta \
--pdbfile ../data/blat-af2.pdb -m ../data/Stiffler_2015_BLAT_ECOLX.mut
escott ../data/aliBLAT.fasta --pdbfile ../data/blat-af2.pdb -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
else
echo "Running EGEMME with a user-provided alignment file."
echo "Running ESCOTT with a user-provided alignment file."
echo "Since a pdb file is not provided, only evolutionary information will be used!"
escott ../data/aliBLAT.fasta -f ../data/aliBLAT.fasta
escott ../data/aliBLAT.fasta
fi
prescott/escott.py
......@@ -970,8 +970,7 @@ def parse_command_line():
required=False, default=None)
parser.add_argument('--normweightmode', dest='normweightmode', type=str, \
help="It can be one of these: 'tjet', 'cv', 'pc',"+\
"max, tjetormax or sstjetormaxtwocomponent. Default is 'tjet'.",
help="It can be one of these: tjet or sstjetormaxtwocomponent. Default is 'tjet'.",
required=False, default="tjet")
parser.add_argument('--verbose', dest='verbose', type=bool, \
......@@ -1002,6 +1001,16 @@ def parse_command_line():
arg_dict = vars(args)
#This part is for just to get rid of an unnecessary argument (-f fastafile.fasta)!
if (args.fastaFile == ''):
args.fastaFile = args.input
if (args.fastaFile != args.input):
print("@>ERROR: There is a problem Houston!")
print("@>ERROR: Your main input file (obligatory file) and the file you")
print("@>ERROR: specify after -f (or --fastaFile) should be identical!")
sys.exit(-1)
check_argument_groups(parser, arg_dict, '--retrievingMethod', ['--blastFile','--fastaFile'])
# Check flag arguments
......
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