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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:
It is easier to find the mutations you are interested in this file. Just
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'
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:
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:
I. An input MSA: AKE_nogaps.fasta
I. An input MSA: AKE_nogaps_short_names.fasta
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
check the row corresponding to the mutation.</p>
</div></blockquote>
</li>
<li><p>myProt_normPred_evolCombi.Preparing</p>
<li><p>myProt_normPred_evolCombi.png</p>
<blockquote>
<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’
......
docs/_build/html/input-preparation.html
......@@ -131,8 +131,16 @@ ls -l
</div>
</li>
</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:
I. An input MSA: AKE_nogaps.fasta
I. An input MSA: AKE_nogaps_short_names.fasta
II. An input PDB: myprotein.pdb</p>
</section>
</section>
......
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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
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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) 21 JUN 2023 16:18
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.6.16) 22 JUN 2023 16:36
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
......@@ -797,16 +797,30 @@ Chapter 2.
Chapter 3.
[7
] [8]
]
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 456.
Underfull \hbox (badness 10000) in paragraph at lines 460--464
[]\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.
LaTeX Font Info: Trying to load font information for TS1+qtm on input line 4
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82.
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Underfull \hbox (badness 5490) in paragraph at lines 550--552
Underfull \hbox (badness 5490) in paragraph at lines 561--563
\T1/qtm/m/n/10 master/ && ./au-to-gen.sh && ./con-fig-ure && make && sudo make
in-stall && sudo ln -s
[]
......@@ -820,11 +834,11 @@ Package rerunfilecheck Info: File `esgemme.out' has not changed.
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docs/_build/latex/esgemme.tex
......@@ -61,7 +61,7 @@
\title{esgemme}
\date{Jun 21, 2023}
\date{Jun 22, 2023}
\release{1.3.0}
\author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}}
......@@ -313,7 +313,7 @@ check the row corresponding to the mutation.
\item {}
\sphinxAtStartPar
myProt\_normPred\_evolCombi.Preparing
myProt\_normPred\_evolCombi.png
\begin{quote}
\sphinxAtStartPar
......@@ -447,8 +447,19 @@ demust removegaps \PYGZhy{}i AKE.fasta \PYGZhy{}o AKE\PYGZus{}nogaps.fasta
\end{enumerate}
\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:
I. An input MSA: AKE\_nogaps.fasta
I. An input MSA: AKE\_nogaps\_short\_names.fasta
II. An input PDB: myprotein.pdb
\sphinxstepscope
......
docs/analysis.rst
......@@ -32,7 +32,7 @@ There are three output files:
It is easier to find the mutations you are interested in this file. Just
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'
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:
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:
I. An input MSA: AKE_nogaps.fasta
I. An input MSA: AKE_nogaps_short_names.fasta
II. An input PDB: myprotein.pdb
......
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