Commit 6dbd9c68 by Mustafa Tekpinar

Simplified escott UI by removing args.fastaFile requirement.

parent e6123f25
......@@ -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
......
......@@ -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
......
......@@ -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/>
......
......@@ -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>
......
# Fdb version 3
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(generated)
"prescott.ilg"
"prescott.ind"
["pdflatex"] 1696926736 "prescott.tex" "prescott.pdf" "prescott" 1696926737
["pdflatex"] 1696952313 "prescott.tex" "prescott.pdf" "prescott" 1696952313
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......@@ -140,13 +140,13 @@
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"sphinxlatexgraphics.sty" 1691571543 4840 a9578332b6f3b35e198751fb632c9b79 ""
......@@ -161,7 +161,7 @@
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"sphinxlatextables.sty" 1691571542 21848 2827eb0b11b99b185a8b77317d3e131c ""
"sphinxmanual.cls" 1691571543 4241 7b0d7a37df7b5715fb0dbd585c52ecdb ""
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"sphinxpackagefootnote.sty" 1691571543 15217 dd26fe418b6fb1b26b18f042a7f43d40 ""
......
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
......
......@@ -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}
......
......@@ -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
......
......@@ -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
......
......@@ -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
......@@ -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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