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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: ...@@ -81,7 +81,7 @@ In this step, we will use only evolutionary information from an MSA file:
.. code:: bash .. 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 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 BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
...@@ -93,8 +93,7 @@ evolutionary information: ...@@ -93,8 +93,7 @@ evolutionary information:
.. code:: bash .. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \ esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
--pdbfile blat-af2.pdb
Predicting the effect of a subset of single point mutations Predicting the effect of a subset of single point mutations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
...@@ -112,15 +111,13 @@ structural information. First, let's do it without structural information: ...@@ -112,15 +111,13 @@ structural information. First, let's do it without structural information:
.. code:: bash .. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \ esgemme aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
-m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way: You can include structural information in the following way:
.. code:: bash .. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \ esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb \
--pdbfile blat-af2.pdb \
-m Stiffler_2015_BLAT_ECOLX.mut -m Stiffler_2015_BLAT_ECOLX.mut
You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output 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> ...@@ -144,7 +144,7 @@ docker container are pointing to the same place.</p>
<section id="obtaining-the-entire-single-point-mutation-landscape"> <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> <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> <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> </pre></div>
</div> </div>
<p>After a few minutes of calculation, you must see at least two files named <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 ...@@ -153,8 +153,7 @@ the entire single point mutational landscape of BLAT protein in these
files.</p> files.</p>
<p>If you want to utilize structural information (highly recommended) as well as <p>If you want to utilize structural information (highly recommended) as well as
evolutionary information:</p> 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> <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
--pdbfile blat-af2.pdb
</pre></div> </pre></div>
</div> </div>
</section> </section>
...@@ -169,13 +168,11 @@ Fortunately, we have an example mut in data folder of ESGEMME repository.</p> ...@@ -169,13 +168,11 @@ Fortunately, we have an example mut in data folder of ESGEMME repository.</p>
</div> </div>
<p>Similar to the previous step, there are two possible ways to do the calculations: with or without <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> 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> <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>esgemme aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
-m Stiffler_2015_BLAT_ECOLX.mut
</pre></div> </pre></div>
</div> </div>
<p>You can include structural information in the following way:</p> <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> <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>
--pdbfile blat-af2.pdb <span class="se">\</span>
-m Stiffler_2015_BLAT_ECOLX.mut -m Stiffler_2015_BLAT_ECOLX.mut
</pre></div> </pre></div>
</div> </div>
......
docs/_build/html/searchindex.js
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\ No newline at end of file \ No newline at end of file
docs/_build/latex/esgemme.fdb_latexmk
# Fdb version 3 # Fdb version 3
["makeindex esgemme.idx"] 1685453958 "esgemme.idx" "esgemme.ind" "esgemme" 1690799114 ["makeindex esgemme.idx"] 1685453958 "esgemme.idx" "esgemme.ind" "esgemme" 1690888279
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(generated) (generated)
"esgemme.ilg" "esgemme.ilg"
"esgemme.ind" "esgemme.ind"
["pdflatex"] 1690799114 "esgemme.tex" "esgemme.pdf" "esgemme" 1690799114 ["pdflatex"] 1690888278 "esgemme.tex" "esgemme.pdf" "esgemme" 1690888279
"/etc/texmf/web2c/texmf.cnf" 1686915816 475 c0e671620eb5563b2130f56340a5fde8 "" "/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 "" "/usr/share/texlive/texmf-dist/fonts/tfm/jknappen/ec/ecrm1000.tfm" 1136768653 3584 adb004a0c8e7c46ee66cad73671f37b4 ""
...@@ -140,31 +140,31 @@ ...@@ -140,31 +140,31 @@
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(generated) (generated)
"esgemme.aux" "esgemme.aux"
"esgemme.idx" "esgemme.idx"
......
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 entering extended mode
restricted \write18 enabled. restricted \write18 enabled.
%&-line parsing enabled. %&-line parsing enabled.
...@@ -799,14 +799,14 @@ Chapter 3. ...@@ -799,14 +799,14 @@ Chapter 3.
] ]
LaTeX Font Info: Trying to load font information for TS1+txtt on input line LaTeX Font Info: Trying to load font information for TS1+txtt on input line
454. 451.
(/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd
File: ts1txtt.fd 2000/12/15 v3.1 File: ts1txtt.fd 2000/12/15 v3.1
) )
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Underfull \hbox (badness 10000) in paragraph at lines 459--463 Underfull \hbox (badness 10000) in paragraph at lines 456--460
[]\T1/qtm/m/n/10 Con-grat-u-la-tions! Now, you have all the in-put files re-qui []\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: red for ES-GEMME: I. An in-put MSA:
[] []
...@@ -814,7 +814,7 @@ red for ES-GEMME: I. An in-put MSA: ...@@ -814,7 +814,7 @@ red for ES-GEMME: I. An in-put MSA:
[8] [8]
Chapter 4. Chapter 4.
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...@@ -845,7 +845,7 @@ usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/t1xbtt.pfb></usr/share/ ...@@ -845,7 +845,7 @@ 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 esgemme.pdf (17 pages, 164984 bytes). Output written on esgemme.pdf (17 pages, 164815 bytes).
PDF statistics: PDF statistics:
259 PDF objects out of 1000 (max. 8388607) 259 PDF objects out of 1000 (max. 8388607)
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docs/_build/latex/esgemme.tex
...@@ -61,7 +61,7 @@ ...@@ -61,7 +61,7 @@
\title{esgemme} \title{esgemme}
\date{Jul 31, 2023} \date{Aug 01, 2023}
\release{1.4.0} \release{1.4.0}
\author{Mustafa Tekpinar} \author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}} \newcommand{\sphinxlogo}{\vbox{}}
...@@ -180,7 +180,7 @@ docker container are pointing to the same place. ...@@ -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: In this step, we will use only evolutionary information from an MSA file:
\begin{sphinxVerbatim}[commandchars=\\\{\}] \begin{sphinxVerbatim}[commandchars=\\\{\}]
esgemme aliBLAT.fasta \PYGZhy{}r input \PYGZhy{}f aliBLAT.fasta esgemme aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta
\end{sphinxVerbatim} \end{sphinxVerbatim}
\sphinxAtStartPar \sphinxAtStartPar
...@@ -194,8 +194,7 @@ If you want to utilize structural information (highly recommended) as well as ...@@ -194,8 +194,7 @@ If you want to utilize structural information (highly recommended) as well as
evolutionary information: evolutionary information:
\begin{sphinxVerbatim}[commandchars=\\\{\}] \begin{sphinxVerbatim}[commandchars=\\\{\}]
esgemme aliBLAT.fasta \PYGZhy{}r input \PYGZhy{}f aliBLAT.fasta \PYG{l+s+se}{\PYGZbs{}} esgemme aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta \PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb
\PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb
\end{sphinxVerbatim} \end{sphinxVerbatim}
...@@ -216,16 +215,14 @@ Similar to the previous step, there are two possible ways to do the calculations ...@@ -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: structural information. First, let’s do it without structural information:
\begin{sphinxVerbatim}[commandchars=\\\{\}] \begin{sphinxVerbatim}[commandchars=\\\{\}]
esgemme aliBLAT.fasta \PYGZhy{}r input \PYGZhy{}f aliBLAT.fasta \PYG{l+s+se}{\PYGZbs{}} esgemme aliBLAT.fasta \PYGZhy{}f aliBLAT.fasta \PYGZhy{}m Stiffler\PYGZus{}2015\PYGZus{}BLAT\PYGZus{}ECOLX.mut
\PYGZhy{}m Stiffler\PYGZus{}2015\PYGZus{}BLAT\PYGZus{}ECOLX.mut
\end{sphinxVerbatim} \end{sphinxVerbatim}
\sphinxAtStartPar \sphinxAtStartPar
You can include structural information in the following way: You can include structural information in the following way:
\begin{sphinxVerbatim}[commandchars=\\\{\}] \begin{sphinxVerbatim}[commandchars=\\\{\}]
esgemme aliBLAT.fasta \PYGZhy{}r input \PYGZhy{}f aliBLAT.fasta \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{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb \PYG{l+s+se}{\PYGZbs{}}
\PYGZhy{}m Stiffler\PYGZus{}2015\PYGZus{}BLAT\PYGZus{}ECOLX.mut \PYGZhy{}m Stiffler\PYGZus{}2015\PYGZus{}BLAT\PYGZus{}ECOLX.mut
\end{sphinxVerbatim} \end{sphinxVerbatim}
......
docs/docker.rst
...@@ -81,7 +81,7 @@ In this step, we will use only evolutionary information from an MSA file: ...@@ -81,7 +81,7 @@ In this step, we will use only evolutionary information from an MSA file:
.. code:: bash .. 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 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 BLAT_normPred_evolCombi.txt and BLAT_normPred_evolCombi.png. You have
...@@ -93,8 +93,7 @@ evolutionary information: ...@@ -93,8 +93,7 @@ evolutionary information:
.. code:: bash .. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \ esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb
--pdbfile blat-af2.pdb
Predicting the effect of a subset of single point mutations Predicting the effect of a subset of single point mutations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
...@@ -112,15 +111,13 @@ structural information. First, let's do it without structural information: ...@@ -112,15 +111,13 @@ structural information. First, let's do it without structural information:
.. code:: bash .. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \ esgemme aliBLAT.fasta -f aliBLAT.fasta -m Stiffler_2015_BLAT_ECOLX.mut
-m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way: You can include structural information in the following way:
.. code:: bash .. code:: bash
esgemme aliBLAT.fasta -r input -f aliBLAT.fasta \ esgemme aliBLAT.fasta -f aliBLAT.fasta --pdbfile blat-af2.pdb \
--pdbfile blat-af2.pdb \
-m Stiffler_2015_BLAT_ECOLX.mut -m Stiffler_2015_BLAT_ECOLX.mut
You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output 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(): ...@@ -942,7 +942,7 @@ def parse_command_line():
retMet_args.add_argument( retMet_args.add_argument(
'-r', '--retrievingMethod', '-r', '--retrievingMethod',
help='mode to retrieve related sequences for conservation levels calculation (input, local or server)', help='mode to retrieve related sequences for conservation levels calculation (input, local or server)',
default='local' default='input'
) )
retMet_args.add_argument( retMet_args.add_argument(
......
examples/example-esgemme-script.sh
...@@ -20,7 +20,7 @@ then ...@@ -20,7 +20,7 @@ then
echo "Running ESGEMME with a user-provided alignment file." echo "Running ESGEMME with a user-provided alignment file."
echo "Using a previously produced prot_jet.res file to check reproducibility!" 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" ] elif [ "$1" == "withpdb" ]
then then
...@@ -28,7 +28,7 @@ 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. #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 "Using blat-af2.pdb for the structural feature calculations!"
echo "Entire mutational map of the protein will be calculated!" 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 --pdbfile ../data/blat-af2.pdb
elif [ "$1" == "withpdb-withmutfile" ] elif [ "$1" == "withpdb-withmutfile" ]
...@@ -37,13 +37,13 @@ then ...@@ -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. #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 "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!" 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 --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 demust compare -i ../data/BLAT_ECOLX_Stiffler_2015_experimental.dat --itype singleline -j BLAT_normPred_evolCombi.txt --jtype singleline
else else
echo "Running EGEMME with a user-provided alignment file." echo "Running EGEMME with a user-provided alignment file."
echo "Since a pdb file is not provided, only evolutionary information will be used!" 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 fi
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