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Update at the end of input-preparation.rst

parent 35c5654f
Showing with 97 additions and 32 deletions
docs/_build/html/_sources/analysis.rst.txt
...@@ -32,7 +32,7 @@ There are three output files: ...@@ -32,7 +32,7 @@ There are three output files:
It is easier to find the mutations you are interested in this file. Just It is easier to find the mutations you are interested in this file. Just
check the row corresponding to the mutation. check the row corresponding to the mutation.
#. myProt_normPred_evolCombi.Preparing #. myProt_normPred_evolCombi.png
This is the image file of the combined results. It selects 'Oranges_r' This is the image file of the combined results. It selects 'Oranges_r'
matplotlib color map by default. You can change it by adding '--colormap turbo_r' matplotlib color map by default. You can change it by adding '--colormap turbo_r'
......
docs/_build/html/_sources/input-preparation.rst.txt
...@@ -66,8 +66,17 @@ structure is to use Colabfold. Let's do this step by step: ...@@ -66,8 +66,17 @@ structure is to use Colabfold. Let's do this step by step:
demust removegaps -i AKE.fasta -o AKE_nogaps.fasta demust removegaps -i AKE.fasta -o AKE_nogaps.fasta
There is one last step to reach our goal. ID and description parts of the
a3m and fasta files are too long. We have to shorten them. We can do that with
.. code:: bash
awk 'BEGIN{FS=" "}{if(NF>1) {printf(">%s\n", $1)}else{print $0}}' AKE_nogaps.fasta > AKE_nogaps_short_names.fasta
# Recheck this command if you can remove extra >
Congratulations! Now, you have all the input files required for ESGEMME: Congratulations! Now, you have all the input files required for ESGEMME:
I. An input MSA: AKE_nogaps.fasta I. An input MSA: AKE_nogaps_short_names.fasta
II. An input PDB: myprotein.pdb II. An input PDB: myprotein.pdb
......
docs/_build/html/analysis.html
...@@ -111,7 +111,7 @@ It is easier to find the mutations you are interested in this file. Just ...@@ -111,7 +111,7 @@ It is easier to find the mutations you are interested in this file. Just
check the row corresponding to the mutation.</p> check the row corresponding to the mutation.</p>
</div></blockquote> </div></blockquote>
</li> </li>
<li><p>myProt_normPred_evolCombi.Preparing</p> <li><p>myProt_normPred_evolCombi.png</p>
<blockquote> <blockquote>
<div><p>This is the image file of the combined results. It selects ‘Oranges_r’ <div><p>This is the image file of the combined results. It selects ‘Oranges_r’
matplotlib color map by default. You can change it by adding ‘–colormap turbo_r’ matplotlib color map by default. You can change it by adding ‘–colormap turbo_r’
......
docs/_build/html/input-preparation.html
...@@ -131,8 +131,16 @@ ls -l ...@@ -131,8 +131,16 @@ ls -l
</div> </div>
</li> </li>
</ol> </ol>
<p>There is one last step to reach our goal. ID and description parts of the
a3m and fasta files are too long. We have to shorten them. We can do that with</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>awk <span class="s1">&#39;BEGIN{FS=&quot; &quot;}{if(NF&gt;1) {printf(&quot;&gt;%s\n&quot;, $1)}else{print $0}}&#39;</span> AKE_nogaps.fasta &gt; AKE_nogaps_short_names.fasta
<span class="c1"># Recheck this command if you can remove extra &gt;</span>
</pre></div>
</div>
</div></blockquote>
<p>Congratulations! Now, you have all the input files required for ESGEMME: <p>Congratulations! Now, you have all the input files required for ESGEMME:
I. An input MSA: AKE_nogaps.fasta I. An input MSA: AKE_nogaps_short_names.fasta
II. An input PDB: myprotein.pdb</p> II. An input PDB: myprotein.pdb</p>
</section> </section>
</section> </section>
......
docs/_build/html/searchindex.js
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docs/_build/latex/esgemme.fdb_latexmk
# Fdb version 3 # Fdb version 3
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(generated) (generated)
"esgemme.ilg" "esgemme.ilg"
"esgemme.ind" "esgemme.ind"
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......
docs/_build/latex/esgemme.fls
...@@ -1078,6 +1078,12 @@ INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/txfonts/t1xtt.tfm ...@@ -1078,6 +1078,12 @@ INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/txfonts/t1xtt.tfm
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docs/_build/latex/esgemme.log
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...@@ -797,16 +797,30 @@ Chapter 2. ...@@ -797,16 +797,30 @@ Chapter 2.
Chapter 3. Chapter 3.
[7 [7
] [8] ]
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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:
[]
[8]
Chapter 4. Chapter 4.
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\T1/qtm/m/n/10 master/ && ./au-to-gen.sh && ./con-fig-ure && make && sudo make \T1/qtm/m/n/10 master/ && ./au-to-gen.sh && ./con-fig-ure && make && sudo make
in-stall && sudo ln -s in-stall && sudo ln -s
[] []
...@@ -820,11 +834,11 @@ Package rerunfilecheck Info: File `esgemme.out' has not changed. ...@@ -820,11 +834,11 @@ Package rerunfilecheck Info: File `esgemme.out' has not changed.
(rerunfilecheck) Checksum: 484D3D84B85998E14AB085F1C3F73044;4691. (rerunfilecheck) Checksum: 484D3D84B85998E14AB085F1C3F73044;4691.
) )
Here is how much of TeX's memory you used: Here is how much of TeX's memory you used:
14619 strings out of 480247 14657 strings out of 480247
232773 string characters out of 5896151 233344 string characters out of 5896151
571746 words of memory out of 5000000 571746 words of memory out of 5000000
32154 multiletter control sequences out of 15000+600000 32185 multiletter control sequences out of 15000+600000
520188 words of font info for 68 fonts, out of 8000000 for 9000 520869 words of font info for 70 fonts, out of 8000000 for 9000
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Output written on esgemme.pdf (17 pages, 157441 bytes). mf-dist/fonts/type1/public/txfonts/t1xtt.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/txfonts/tcxtt.pfb>
Output written on esgemme.pdf (17 pages, 165015 bytes).
PDF statistics: PDF statistics:
255 PDF objects out of 1000 (max. 8388607) 264 PDF objects out of 1000 (max. 8388607)
219 compressed objects within 3 object streams 225 compressed objects within 3 object streams
51 named destinations out of 1000 (max. 500000) 51 named destinations out of 1000 (max. 500000)
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docs/_build/latex/esgemme.tex
...@@ -61,7 +61,7 @@ ...@@ -61,7 +61,7 @@
\title{esgemme} \title{esgemme}
\date{Jun 21, 2023} \date{Jun 22, 2023}
\release{1.3.0} \release{1.3.0}
\author{Mustafa Tekpinar} \author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}} \newcommand{\sphinxlogo}{\vbox{}}
...@@ -313,7 +313,7 @@ check the row corresponding to the mutation. ...@@ -313,7 +313,7 @@ check the row corresponding to the mutation.
\item {} \item {}
\sphinxAtStartPar \sphinxAtStartPar
myProt\_normPred\_evolCombi.Preparing myProt\_normPred\_evolCombi.png
\begin{quote} \begin{quote}
\sphinxAtStartPar \sphinxAtStartPar
...@@ -447,8 +447,19 @@ demust removegaps \PYGZhy{}i AKE.fasta \PYGZhy{}o AKE\PYGZus{}nogaps.fasta ...@@ -447,8 +447,19 @@ demust removegaps \PYGZhy{}i AKE.fasta \PYGZhy{}o AKE\PYGZus{}nogaps.fasta
\end{enumerate} \end{enumerate}
\sphinxAtStartPar \sphinxAtStartPar
There is one last step to reach our goal. ID and description parts of the
a3m and fasta files are too long. We have to shorten them. We can do that with
\begin{quote}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
awk \PYG{l+s+s1}{\PYGZsq{}BEGIN\PYGZob{}FS=\PYGZdq{} \PYGZdq{}\PYGZcb{}\PYGZob{}if(NF\PYGZgt{}1) \PYGZob{}printf(\PYGZdq{}\PYGZgt{}\PYGZpc{}s\PYGZbs{}n\PYGZdq{}, \PYGZdl{}1)\PYGZcb{}else\PYGZob{}print \PYGZdl{}0\PYGZcb{}\PYGZcb{}\PYGZsq{}} AKE\PYGZus{}nogaps.fasta \PYGZgt{} AKE\PYGZus{}nogaps\PYGZus{}short\PYGZus{}names.fasta
\PYG{c+c1}{\PYGZsh{} Recheck this command if you can remove extra \PYGZgt{}}
\end{sphinxVerbatim}
\end{quote}
\sphinxAtStartPar
Congratulations! Now, you have all the input files required for ESGEMME: Congratulations! Now, you have all the input files required for ESGEMME:
I. An input MSA: AKE\_nogaps.fasta I. An input MSA: AKE\_nogaps\_short\_names.fasta
II. An input PDB: myprotein.pdb II. An input PDB: myprotein.pdb
\sphinxstepscope \sphinxstepscope
......
docs/analysis.rst
...@@ -32,7 +32,7 @@ There are three output files: ...@@ -32,7 +32,7 @@ There are three output files:
It is easier to find the mutations you are interested in this file. Just It is easier to find the mutations you are interested in this file. Just
check the row corresponding to the mutation. check the row corresponding to the mutation.
#. myProt_normPred_evolCombi.Preparing #. myProt_normPred_evolCombi.png
This is the image file of the combined results. It selects 'Oranges_r' This is the image file of the combined results. It selects 'Oranges_r'
matplotlib color map by default. You can change it by adding '--colormap turbo_r' matplotlib color map by default. You can change it by adding '--colormap turbo_r'
......
docs/input-preparation.rst
...@@ -66,8 +66,17 @@ structure is to use Colabfold. Let's do this step by step: ...@@ -66,8 +66,17 @@ structure is to use Colabfold. Let's do this step by step:
demust removegaps -i AKE.fasta -o AKE_nogaps.fasta demust removegaps -i AKE.fasta -o AKE_nogaps.fasta
There is one last step to reach our goal. ID and description parts of the
a3m and fasta files are too long. We have to shorten them. We can do that with
.. code:: bash
awk 'BEGIN{FS=" "}{if(NF>1) {printf(">%s\n", $1)}else{print $0}}' AKE_nogaps.fasta > AKE_nogaps_short_names.fasta
# Recheck this command if you can remove extra >
Congratulations! Now, you have all the input files required for ESGEMME: Congratulations! Now, you have all the input files required for ESGEMME:
I. An input MSA: AKE_nogaps.fasta I. An input MSA: AKE_nogaps_short_names.fasta
II. An input PDB: myprotein.pdb II. An input PDB: myprotein.pdb
......
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