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Commit fdc001bc by Mustafa Tekpinar
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Changed default --retrievingMethod from local to input.

parent 21f4813c
Showing with 48 additions and 60 deletions
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
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta
esgemme aliBLAT.fasta -f 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
......@@ -93,8 +93,7 @@ evolutionary information:
.. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb
esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
Predicting the effect of a subset of single point mutations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
......@@ -112,15 +111,13 @@ structural information. First, let's do it without structural information:
.. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
-m Stiffler_2015_BLAT_ECOLX.mut
esgemme aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way:
.. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
esgemme aliBLAT.fasta -f 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
......@@ -144,7 +144,7 @@ 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>esgemme aliBLAT.fasta -r input -f aliBLAT.fasta
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>esgemme aliBLAT.fasta -f aliBLAT.fasta
</pre></div>
</div>
<p>After a few minutes of calculation, you must see at least two files named
......@@ -153,8 +153,7 @@ 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>esgemme aliBLAT.fasta -r input -f aliBLAT.fasta <span class="se">\</span>
--pdbfile blat-af2.pdb
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
</pre></div>
</div>
</section>
......@@ -169,13 +168,11 @@ Fortunately, we have an example mut in data folder of ESGEMME 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>esgemme aliBLAT.fasta -r input -f aliBLAT.fasta <span class="se">\</span>
-m Stiffler_2015_BLAT_ECOLX.mut
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>esgemme aliBLAT.fasta -f 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>esgemme aliBLAT.fasta -r input -f aliBLAT.fasta <span class="se">\</span>
--pdbfile blat-af2.pdb <span class="se">\</span>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb <span class="se">\</span>
-m Stiffler_2015_BLAT_ECOLX.mut
</pre></div>
</div>
......
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docs/_build/latex/esgemme.fdb_latexmk
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docs/_build/latex/esgemme.log
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.6.16) 31 JUL 2023 12:25
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.6.16) 1 AUG 2023 13:11
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
......@@ -799,14 +799,14 @@ Chapter 3.
]
LaTeX Font Info: Trying to load font information for TS1+txtt on input line
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File: ts1txtt.fd 2000/12/15 v3.1
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(Font) Font shape `T1/txtt/m/sl' tried instead on input line 455.
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[]\T1/qtm/m/n/10 Con-grat-u-la-tions! Now, you have all the in-put files re-qui
red for ES-GEMME: I. An in-put MSA:
[]
......@@ -814,7 +814,7 @@ red for ES-GEMME: I. An in-put MSA:
[8]
Chapter 4.
LaTeX Font Info: Trying to load font information for TS1+qtm on input line 4
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texlive/texmf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/tex
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Output written on esgemme.pdf (17 pages, 164984 bytes).
Output written on esgemme.pdf (17 pages, 164815 bytes).
PDF statistics:
259 PDF objects out of 1000 (max. 8388607)
220 compressed objects within 3 object streams
......
docs/_build/latex/esgemme.tex
......@@ -61,7 +61,7 @@
\title{esgemme}
\date{Jul 31, 2023}
\date{Aug 01, 2023}
\release{1.4.0}
\author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}}
......@@ -180,7 +180,7 @@ docker container are pointing to the same place.
In this step, we will use only evolutionary information from an MSA file:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
esgemme aliBLAT.fasta \PYGZhy{}r input \PYGZhy{}f aliBLAT.fasta
esgemme aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta
\end{sphinxVerbatim}
\sphinxAtStartPar
......@@ -194,8 +194,7 @@ If you want to utilize structural information (highly recommended) as well as
evolutionary information:
\begin{sphinxVerbatim}[commandchars=\\\{\}]
esgemme aliBLAT.fasta \PYGZhy{}r input \PYGZhy{}f aliBLAT.fasta \PYG{l+s+se}{\PYGZbs{}}
\PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb
esgemme aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta \PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb
\end{sphinxVerbatim}
......@@ -216,16 +215,14 @@ 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=\\\{\}]
esgemme aliBLAT.fasta \PYGZhy{}r input \PYGZhy{}f aliBLAT.fasta \PYG{l+s+se}{\PYGZbs{}}
\PYGZhy{}m Stiffler\PYGZus{}2015\PYGZus{}BLAT\PYGZus{}ECOLX.mut
esgemme aliBLAT.fasta \PYGZhy{}f 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=\\\{\}]
esgemme aliBLAT.fasta \PYGZhy{}r input \PYGZhy{}f aliBLAT.fasta \PYG{l+s+se}{\PYGZbs{}}
\PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb \PYG{l+s+se}{\PYGZbs{}}
esgemme aliBLAT.fasta \PYGZhy{}f 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
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta
esgemme aliBLAT.fasta -f 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
......@@ -93,8 +93,7 @@ evolutionary information:
.. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb
esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
Predicting the effect of a subset of single point mutations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
......@@ -112,15 +111,13 @@ structural information. First, let's do it without structural information:
.. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
-m Stiffler_2015_BLAT_ECOLX.mut
esgemme aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way:
.. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
esgemme aliBLAT.fasta -f 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
......
esgemme/esgemme.py
......@@ -942,7 +942,7 @@ def parse_command_line():
retMet_args.add_argument(
'-r', '--retrievingMethod',
help='mode to retrieve related sequences for conservation levels calculation (input, local or server)',
default='local'
default='input'
)
retMet_args.add_argument(
......
examples/example-esgemme-script.sh
......@@ -20,7 +20,7 @@ then
echo "Running ESGEMME with a user-provided alignment file."
echo "Using a previously produced prot_jet.res file to check reproducibility!"
esgemme ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta --jetfile ../data/BLAT_jet.res
esgemme ../data/aliBLAT.fasta -f ../data/aliBLAT.fasta --jetfile ../data/BLAT_jet.res
elif [ "$1" == "withpdb" ]
then
......@@ -28,7 +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!"
esgemme ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
esgemme ../data/aliBLAT.fasta -f ../data/aliBLAT.fasta \
--pdbfile ../data/blat-af2.pdb
elif [ "$1" == "withpdb-withmutfile" ]
......@@ -37,13 +37,13 @@ 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!"
esgemme ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
esgemme ../data/aliBLAT.fasta -f ../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 "Since a pdb file is not provided, only evolutionary information will be used!"
esgemme ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta
esgemme ../data/aliBLAT.fasta -f ../data/aliBLAT.fasta
fi
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