Update at the end of input-preparation.rst

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>

docs/_build/latex/esgemme.fdb_latexmk

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   (generated)
   "esgemme.ilg"
   "esgemme.ind"
-["pdflatex"] 1687357098 "esgemme.tex" "esgemme.pdf" "esgemme" 1687357098
+["pdflatex"] 1687444567 "esgemme.tex" "esgemme.pdf" "esgemme" 1687444567
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+  "/usr/share/texlive/texmf-dist/fonts/type1/public/txfonts/tcxtt.pfb" 1136849748 19223 eef9d7a2591262b80fbbebb9e94dc374 ""
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-  "esgemme.toc" 1687357098 1865 658ec1920d49935d82736b327430eefc "pdflatex"
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docs/_build/latex/esgemme.fls

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 INPUT /usr/share/texmf/fonts/tfm/public/tex-gyre/ec-qhvr.tfm
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 INPUT /usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
 INPUT /usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd
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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 
+455.
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+
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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.
 LaTeX Font Info:    Trying to load font information for TS1+qtm on input line 4
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 ]
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+Underfull \hbox (badness 5490) in paragraph at lines 561--563
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 in-stall && sudo ln -s
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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