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Commit 3509620e by Mustafa Tekpinar
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Updated the documentation.

parent 7298ac7d
Showing with 1235 additions and 1853 deletions
computePred.R
......@@ -85,10 +85,27 @@ if ((normWeightMode=="max")){
}
}
}else if (normWeightMode=="tjetormax"){
print("Using tjetormax")
for (row in 1:nrow(jet)) {
if(sum(colnames(jet)=="traceMax")==1){
if((jet[row, "traceMax"]>jet[row, "pc"]) & (jet[row, "traceMax"]>jet[row, "cv"])){
trace<-append(trace, jet[row, "traceMax"])
}else{
trace<-append(trace, max((jet[row, "traceMax"]+jet[row, "pc"])/2.0, max((jet[row, "traceMax"]+jet[row, "cv"])/2.0, (jet[row, "pc"]+jet[row, "cv"])/2.0 )))
}
}else{
if((jet[row, "trace"]>jet[row, "pc"]) & (jet[row, "trace"]>jet[row, "cv"])){
trace<-append(trace, jet[row, "trace"])
}else{
trace<-append(trace, max((jet[row, "trace"]+jet[row, "pc"])/2.0, max((jet[row, "trace"]+jet[row, "cv"])/2.0, (jet[row, "pc"]+jet[row, "cv"])/2.0 )))
}
}
}
}else{
print("ERROR: Unknown --normWeightMode selected!")
print("It can only be 'tjet', 'pc', 'cv',")
print("'max' or 'sstjetormax'!")
print("'max', 'tjetormax' or 'sstjetormax'!")
}
print(trace)
#####################################################################################################################
......
docs/_build/.buildinfo deleted 100644 → 0
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: ee0c3cda5e96b708cc4747fb117bcc00
tags: 645f666f9bcd5a90fca523b33c5a78b7
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docs/_build/Makefile deleted 100644 → 0
# Makefile for Sphinx LaTeX output
ALLDOCS = $(basename $(wildcard *.tex))
ALLPDF = $(addsuffix .pdf,$(ALLDOCS))
ALLDVI = $(addsuffix .dvi,$(ALLDOCS))
ALLXDV =
ALLPS = $(addsuffix .ps,$(ALLDOCS))
ALLIMGS = $(wildcard *.png *.gif *.jpg *.jpeg)
# Prefix for archive names
ARCHIVEPREFIX =
# Additional LaTeX options (passed via variables in latexmkrc/latexmkjarc file)
export LATEXOPTS ?=
# Additional latexmk options
LATEXMKOPTS ?=
# format: pdf or dvi (used only by archive targets)
FMT = pdf
LATEX = latexmk -dvi
PDFLATEX = latexmk -pdf -dvi- -ps-
%.png %.gif %.jpg %.jpeg: FORCE_MAKE
extractbb '$@'
%.dvi: %.tex FORCE_MAKE
$(LATEX) $(LATEXMKOPTS) '$<'
%.ps: %.dvi
dvips '$<'
%.pdf: %.tex FORCE_MAKE
$(PDFLATEX) $(LATEXMKOPTS) '$<'
all: $(ALLPDF)
all-dvi: $(ALLDVI)
all-ps: $(ALLPS)
all-pdf: $(ALLPDF)
zip: all-$(FMT)
mkdir $(ARCHIVEPREFIX)docs-$(FMT)
cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
zip -q -r -9 $(ARCHIVEPREFIX)docs-$(FMT).zip $(ARCHIVEPREFIX)docs-$(FMT)
rm -r $(ARCHIVEPREFIX)docs-$(FMT)
tar: all-$(FMT)
mkdir $(ARCHIVEPREFIX)docs-$(FMT)
cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
tar cf $(ARCHIVEPREFIX)docs-$(FMT).tar $(ARCHIVEPREFIX)docs-$(FMT)
rm -r $(ARCHIVEPREFIX)docs-$(FMT)
gz: tar
gzip -9 < $(ARCHIVEPREFIX)docs-$(FMT).tar > $(ARCHIVEPREFIX)docs-$(FMT).tar.gz
bz2: tar
bzip2 -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
xz: tar
xz -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
clean:
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.PHONY: all all-pdf all-dvi all-ps clean zip tar gz bz2 xz
.PHONY: FORCE_MAKE
\ No newline at end of file
docs/_build/_sources/docker.rst.txt deleted 100644 → 0
Using ESGEMME via Docker
========================
Requirements
------------
You need to have docker installed on your machine. You can consult the
following page for this: https://docs.docker.com/get-docker/
I am assuming some basic familiarity with Linux/Unix/MacOS terminal
commands.
Let’s start our favorite terminal app.
You must to create a folder called docker-tutorial and go to that empty
folder:
.. code:: bash
mkdir docker-tutorial
cd docker-tutorial
Getting the input data
----------------------
Let’s download the sample data provided in the ESGEMME repository for
this exercise. First, we will download the multiple sequence alignment
file in fasta format:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
If you don’t have wget, you can try the same command with curl:
.. code:: bash
curl http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/aliBLAT.fasta
Please verify that the aliBLAT.fasta file is in the folder.
Now, we will download the PDB (Protein Databank) file for BLAT:
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/blat-af2.pdb
Single point mutation calculations
----------------------------------
In order to make sure that the docker is installed:
.. code:: bash
sudo docker -h
If it shows you a list of options, you are on a good track. On MacOS,
you may not need ‘sudo’ word before the docker command at all.
.. code:: bash
sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample \
tekpinar/esgemme-docker:v1.3.0
You are in the container (your virtual operating system) now. You
created a folder called myexample in your container with the previous
command. Let’s change to that folder.
.. code:: bash
cd ../myexample/
When you check the data in that folder with ‘ls’ command, you are
supposed to see aliBLAT.fasta and blat-af2.pdb files. Basically, your
docker-tutorial folder on the host system and myexample folder on the
docker container are pointing to the same place.
Obtaining the entire single point mutation landscape
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In this step, we will use only evolutionary information from an MSA file:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -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
the entire single point mutational landscape of BLAT protein in these
files.
If you want to utilize structural information (highly recommended) as well as
evolutionary information:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
--normweightmode sstjetormax
Obtaining the effect of a subset of single point mutations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If you are interested in only a bunch of single point mutations,
you have to prepare a mut file. The format is a simple text file and
each line contains a single point mutation such as D26A....
Fortunately, we have an example mut in data folder of ESGEMME repository.
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/master/data/Stiffler_2015_BLAT_ECOLX.mut
Similar to the previous step, there are two possible ways to do the calculations: with or without
structural information. First, without structural information:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
-m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
--normweightmode sstjetormax \
-m Stiffler_2015_BLAT_ECOLX.mut
You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output
format is completely different from the entire mutational landscape scanning file.
Each line of this file is a mutation and its predicted effect separated by a space.
In addition, you won't have a png file like in the previous case.
Multiple point mutation calculations
------------------------------------
Sometimes, we need to see effects of double or triple mutations. ESGEMME can
perform calculations if you provide a mut file. In this case, the mut file must
have the following format:
.. code:: bash
E26D:Y44R
E56N:A77F:H94V
The first line of the text file is impact of a double mutations and the second
line is the impact of the triple mutations. As you can see, the mutations are
separated by a colon(:) character.
The output file will be in a similar format. Each line will contain the multiple
mutation and its predicted effect, separated by a space.
Running several jobs using docker
---------------------------------
docs/_build/_sources/index.rst.txt deleted 100644 → 0
.. esgemme documentation master file, created by
sphinx-quickstart on Fri May 5 13:52:13 2023.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to esgemme's documentation!
===================================
.. toctree::
:maxdepth: 2
:caption: Contents:
docker.rst
analysis.rst
installation.rst
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
docs/_build/_static/custom.css deleted 100644 → 0
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docs/_build/_static/documentation_options.js deleted 100644 → 0
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docs/_build/footnotehyper-sphinx.sty deleted 100644 → 0
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}%
}%
\def\FNH@startnote{%
\hsize\FNH@colwidth
\interlinepenalty\interfootnotelinepenalty
\reset@font\footnotesize
\floatingpenalty\@MM
\@parboxrestore
\protected@edef\@currentlabel{\csname p@\@mpfn\endcsname\@thefnmark}%
\color@begingroup
}%
\def\FNH@endnote{\color@endgroup}%
\def\FNH@savenotes{%
\begingroup
\ifFNH@savingnotes\else
\FNH@savingnotestrue
\let\@footnotetext \FNH@hyper@fntext
\let\@mpfootnotetext \FNH@hyper@fntext
\let\H@@mpfootnotetext\FNH@nohyp@fntext
\FNH@width\columnwidth
\let\FNH@colwidth\FNH@width
\global\setbox\FNH@notes\box\voidb@x
\let\FNH@thempfn\thempfn
\let\FNH@mpfn\@mpfn
\ifx\@minipagerestore\relax\let\@minipagerestore\@empty\fi
\expandafter\def\expandafter\@minipagerestore\expandafter{%
\@minipagerestore
\let\thempfn\FNH@thempfn
\let\@mpfn\FNH@mpfn
}%
\fi
}%
\def\FNH@spewnotes {%
\endgroup
\ifFNH@savingnotes\else
\ifvoid\FNH@notes\else
\begingroup
\let\@makefntext\@empty
\let\@finalstrut\@gobble
\let\rule\@gobbletwo
\FNH@H@@footnotetext{\unvbox\FNH@notes}%
\endgroup
\fi
\fi
}%
\def\FNH@footnote@envname {footnote}%
\def\FNH@footnotetext@envname{footnotetext}%
\def\FNH@footnote{%
% this line added for Sphinx:
\spx@opt@BeforeFootnote
\ifx\@currenvir\FNH@footnote@envname
\expandafter\FNH@footnoteenv
\else
\expandafter\FNH@latex@footnote
\fi
}%
\def\FNH@footnoteenv{%
% this line added for Sphinx (footnotes in parsed literal blocks):
\catcode13=5 \sphinxunactivateextrasandspace
\@ifnextchar[%
\FNH@footnoteenv@i %]
{\stepcounter\@mpfn
\protected@xdef\@thefnmark{\thempfn}%
\@footnotemark
\def\FNH@endfntext@fntext{\@footnotetext}%
\FNH@startfntext}%
}%
\def\FNH@footnoteenv@i[#1]{%
\begingroup
\csname c@\@mpfn\endcsname #1\relax
\unrestored@protected@xdef\@thefnmark{\thempfn}%
\endgroup
\@footnotemark
\def\FNH@endfntext@fntext{\@footnotetext}%
\FNH@startfntext
}%
\def\FNH@footnotetext{%
\ifx\@currenvir\FNH@footnotetext@envname
\expandafter\FNH@footnotetextenv
\else
\expandafter\FNH@latex@footnotetext
\fi
}%
\def\FNH@footnotetextenv{%
\@ifnextchar[%
\FNH@footnotetextenv@i %]
{\protected@xdef\@thefnmark{\thempfn}%
\def\FNH@endfntext@fntext{\@footnotetext}%
\FNH@startfntext}%
}%
\def\FNH@footnotetextenv@i[#1]{%
\begingroup
\csname c@\@mpfn\endcsname #1\relax
\unrestored@protected@xdef\@thefnmark{\thempfn}%
\endgroup
\ifFNH@savingnotes
\def\FNH@endfntext@fntext{\FNH@nohyp@fntext}%
\else
\def\FNH@endfntext@fntext{\FNH@H@@footnotetext}%
\fi
\FNH@startfntext
}%
\def\FNH@startfntext{%
\setbox\z@\vbox\bgroup
\FNH@startnote
\FNH@prefntext
\rule\z@\footnotesep\ignorespaces
}%
\def\FNH@endfntext {%
\@finalstrut\strutbox
\FNH@postfntext
\FNH@endnote
\egroup
\begingroup
\let\@makefntext\@empty\let\@finalstrut\@gobble\let\rule\@gobbletwo
\FNH@endfntext@fntext {\unvbox\z@}%
\endgroup
}%
\AtBeginDocument{%
\let\FNH@@makefntext\@makefntext
\ifx\@makefntextFB\@undefined
\expandafter\@gobble\else\expandafter\@firstofone\fi
{\ifFBFrenchFootnotes \let\FNH@@makefntext\@makefntextFB \else
\let\FNH@@makefntext\@makefntextORI\fi}%
\expandafter\FNH@check@a\FNH@@makefntext{1.2!3?4,}%
\FNH@@@1.2!3?4,\FNH@@@\relax
}%
\long\def\FNH@check@a #11.2!3?4,#2\FNH@@@#3{%
\ifx\relax#3\expandafter\@firstoftwo\else\expandafter\@secondoftwo\fi
\FNH@bad@makefntext@alert
{\def\FNH@prefntext{#1}\def\FNH@postfntext{#2}\FNH@check@b}%
}%
\def\FNH@check@b #1\relax{%
\expandafter\expandafter\expandafter\FNH@check@c
\expandafter\meaning\expandafter\FNH@prefntext
\meaning\FNH@postfntext1.2!3?4,\FNH@check@c\relax
}%
\def\FNH@check@c #11.2!3?4,#2#3\relax{%
\ifx\FNH@check@c#2\expandafter\@gobble\fi\FNH@bad@makefntext@alert
}%
% slight reformulation for Sphinx
\def\FNH@bad@makefntext@alert{%
\PackageWarningNoLine{footnotehyper-sphinx}%
{Footnotes will be sub-optimal, sorry. This is due to the document class or^^J
some package modifying macro \string\@makefntext.^^J
You can try to report this incompatibility at^^J
https://github.com/sphinx-doc/sphinx with this info:}%
\typeout{\meaning\@makefntext}%
\let\FNH@prefntext\@empty\let\FNH@postfntext\@empty
}%
% this macro from original footnote.sty is not used anymore by Sphinx
% but for simplicity sake let's just keep it as is
\def\makesavenoteenv{\@ifnextchar[\FNH@msne@ii\FNH@msne@i}%]
\def\FNH@msne@i #1{%
\expandafter\let\csname FNH$#1\expandafter\endcsname %$
\csname #1\endcsname
\expandafter\let\csname endFNH$#1\expandafter\endcsname %$
\csname end#1\endcsname
\FNH@msne@ii[#1]{FNH$#1}%$
}%
\def\FNH@msne@ii[#1]#2{%
\expandafter\edef\csname#1\endcsname{%
\noexpand\savenotes
\expandafter\noexpand\csname#2\endcsname
}%
\expandafter\edef\csname end#1\endcsname{%
\expandafter\noexpand\csname end#2\endcsname
\noexpand\expandafter
\noexpand\spewnotes
\noexpand\if@endpe\noexpand\@endpetrue\noexpand\fi
}%
}%
% end of footnotehyper 2017/02/16 v0.99
% some extras for Sphinx :
% \sphinxfootnotemark: usable in section titles and silently removed from TOCs.
\def\sphinxfootnotemark [#1]%
{\ifx\thepage\relax\else\protect\spx@opt@BeforeFootnote
\protect\footnotemark[#1]\fi}%
\AtBeginDocument{%
% let hyperref less complain
\pdfstringdefDisableCommands{\def\sphinxfootnotemark [#1]{}}%
% to obtain hyperlinked footnotes in longtable environment we must replace
% hyperref's patch of longtable's patch of \@footnotetext by our own
\let\LT@p@ftntext\FNH@hyper@fntext
% this *requires* longtable to be used always wrapped in savenotes environment
}%
\endinput
%%
%% End of file `footnotehyper-sphinx.sty'.
docs/_build/html/.buildinfo
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 2b63f8059aa2ad903c52bf6ea56d7c9d
config: 1d56d17901c6f429146d20c07a73dc21
tags: 645f666f9bcd5a90fca523b33c5a78b7
docs/_build/html/_sources/docker.rst.txt
......@@ -12,7 +12,7 @@ commands.
Let’s start our favorite terminal app.
You must to create a folder called docker-tutorial and go to that empty
You must create a folder called docker-tutorial and go to that empty
folder:
.. code:: bash
......@@ -20,8 +20,8 @@ folder:
mkdir docker-tutorial
cd docker-tutorial
Getting the input data
----------------------
Getting the example input data
------------------------------
Let’s download the sample data provided in the ESGEMME repository for
this exercise. First, we will download the multiple sequence alignment
......@@ -45,21 +45,22 @@ Now, we will download the PDB (Protein Databank) file for BLAT:
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/blob/master/data/blat-af2.pdb
Running a calculation for a single sequence/protein
---------------------------------------------------
Single point mutation calculations
----------------------------------
In order to make sure that the docker is installed:
.. code:: bash
docker -h
sudo docker -h
If it shows you a list of options, you are on a good track. On MacOS,
you may not need ‘sudo’ word before the docker command at all.
.. code:: bash
sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample tekpinar/esgemme-docker:v1.3.0
sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample \
tekpinar/esgemme-docker:v1.3.0
You are in the container (your virtual operating system) now. You
created a folder called myexample in your container with the previous
......@@ -74,16 +75,77 @@ supposed to see aliBLAT.fasta and blat-af2.pdb files. Basically, your
docker-tutorial folder on the host system and myexample folder on the
docker container are pointing to the same place.
One last step and we are done:
Obtaining the entire single point mutation landscape
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In this step, we will use only evolutionary information from an MSA file:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-af2.pdb
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta
After a few minutes of calculation, you must see 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
the entire single point mutational landscape of BLAT protein in these
files.
If you want to utilize structural information (highly recommended) as well as
evolutionary information:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
--normweightmode sstjetormax
Predicting the effect of a subset of single point mutations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If you are interested in only a bunch of single point mutations,
you have to prepare a mut file. The format is a simple text file and
each line contains a single point mutation such as D26A....
Fortunately, we have an example mut in data folder of ESGEMME repository.
.. code:: bash
wget http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME/raw/master/data/Stiffler_2015_BLAT_ECOLX.mut
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:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
-m Stiffler_2015_BLAT_ECOLX.mut
You can include structural information in the following way:
.. code:: bash
python $ESGEMME_PATH/esgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta \
--pdbfile blat-af2.pdb \
--normweightmode sstjetormax \
-m Stiffler_2015_BLAT_ECOLX.mut
You will have BLAT_normPred_evolCombi.txt file in your folder. However, the output
format is completely different from the entire mutational landscape scanning file.
Each line of this file is a mutation and its predicted effect separated by a space.
In addition, you won't have a png file like in the previous case.
Multiple point mutation calculations
------------------------------------
Sometimes, we need to see effects of double or triple mutations. ESGEMME can
perform calculations if you provide a mut file. In this case, the mut file must
have the following format:
.. code:: bash
E26D:Y44R
E56N:A77F:H94V
The first line of the text file is impact of a double mutation and the second
line is the impact of the triple mutations. As you can see, the mutations are
separated by a colon(:) character.
The output file will be in a similar format. Each line will contain the multiple
mutation and its predicted effect, separated by a space.
Running several jobs using docker
---------------------------------
docs/_build/html/_sources/index.rst.txt
......@@ -11,6 +11,9 @@ Welcome to esgemme's documentation!
:caption: Contents:
docker.rst
analysis.rst
input-preparation.rst
installation.rst
Indices and tables
==================
......
docs/_build/html/_sources/input-preparation.rst.txt 0 → 100644
Preparing Your Own Input
========================
Preparing Your Input MSA and PDB with Colabfold
-----------------------------------------------
You have a fasta file for your protein of interest and you want to understand
impact of (certain) mutations.
Before starting, please make sure that your fasta file does not contain a gap.
The quickest method to obtain both multiple sequence alignment and a protein
structure is to use Colabfold. Let's do this step by step:
1. Let's go the Colabfold web site:
https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
Sign in using your gmail account.
2. Click on the 'Connect' button on the top right hand side.
3. Clean 'query_sequence' box and paste your sequence to the 'query_sequence' box.
For me, I selected adenylate kinase (AKE) as my example fasta sequence
(https://www.rcsb.org/fasta/entry/4AKE/display).
4. Change the 'jobname' to something that makes more sense to you.
5. Go to the menu bar of your 'AlphaFold2.ipynb' notebook, where 'File, Edit,
View, Insert, Runtime, Tools, Help' are listed. Click on the Runtime and
select 'Run all'.
6. This process make take from a few minutes to a few hours depending on your
protein size. It will give you an a3m file and up to 5 PDB models. Put these
files in a clean folder and change the directory to that folder in your
terminal.
7. Unfortunately, a3m file is not in fasta format and it contains gap columns.
We have to clean those gaps. We can do that with a GUI program like Ugene
or Jalview. However, it is a labor intensive procedure. Here, I will use a
small tool that I developed and added to the ESGEMME docker image that I created.
8. Start the docker image with the following command:
.. code:: bash
sudo docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/myexample \
tekpinar/esgemme-docker:v1.3.0
9. Now, change the directory to myexample folder.
.. code:: bash
cd ../myexample/
ls -l
We are supposed to see our a3m and pdb files in this folder.
10. Let's use a small script from hhsuite to convert a3m file to fasta format.
.. code:: bash
reformat.pl a3m fas AKE.a3m AKE.fasta
11. Final step and we are there:
.. code:: bash
demust removegaps -i AKE.fasta -o AKE_nogaps.fasta
Congratulations! Now, you have all the input files required for ESGEMME:
I. An input MSA: AKE_nogaps.fasta
II. An input PDB: myprotein.pdb
docs/_build/_sources/installation.rst.txt → docs/_build/html/_sources/installation.rst.txt
......@@ -9,12 +9,16 @@ steps required to install it from the source.
Installing the dependencies:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ESGEMME has the following external dependencies: \* Joint Evolutionary
Trees: http://www.lcqb.upmc.fr/JET2/ and its dependencies: - naccess:
http://www.bioinf.manchester.ac.uk/naccess/ - muscle:
https://www.drive5.com/muscle/ \*\* \* seqinr R package:
https://cran.r-project.org/web/packages/seqinr/index.html \* dssp for
secondary structure prediction.
ESGEMME has the following external dependencies:
* Joint Evolutionary Trees: http://www.lcqb.upmc.fr/JET2/ and its dependencies:
* java
* naccess: http://www.bioinf.manchester.ac.uk/naccess/
* muscle: https://www.drive5.com/muscle/
* seqinr R package: https://cran.r-project.org/web/packages/seqinr/index.html
* dssp for secondary structure prediction.
These tools should be installed to be able to use ESGEMME.
......
docs/_build/_static/doctools.js → docs/_build/html/_static/_sphinx_javascript_frameworks_compat.js
/*
* doctools.js
* ~~~~~~~~~~~
*
* Sphinx JavaScript utilities for all documentation.
/* Compatability shim for jQuery and underscores.js.
*
* :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
/**
* select a different prefix for underscore
*/
$u = _.noConflict();
/**
* make the code below compatible with browsers without
* an installed firebug like debugger
if (!window.console || !console.firebug) {
var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
"dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
"profile", "profileEnd"];
window.console = {};
for (var i = 0; i < names.length; ++i)
window.console[names[i]] = function() {};
}
* Copyright Sphinx contributors
* Released under the two clause BSD licence
*/
/**
* small helper function to urldecode strings
*
* See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
*/
jQuery.urldecode = function(x) {
return decodeURIComponent(x).replace(/\+/g, ' ');
if (!x) {
return x
}
return decodeURIComponent(x.replace(/\+/g, ' '));
};
/**
......@@ -139,177 +121,3 @@ if (!jQuery.browser) {
jQuery.browser = {};
jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
}
/**
* Small JavaScript module for the documentation.
*/
var Documentation = {
init : function() {
this.fixFirefoxAnchorBug();
this.highlightSearchWords();
this.initIndexTable();
if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
this.initOnKeyListeners();
}
},
/**
* i18n support
*/
TRANSLATIONS : {},
PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
LOCALE : 'unknown',
// gettext and ngettext don't access this so that the functions
// can safely bound to a different name (_ = Documentation.gettext)
gettext : function(string) {
var translated = Documentation.TRANSLATIONS[string];
if (typeof translated === 'undefined')
return string;
return (typeof translated === 'string') ? translated : translated[0];
},
ngettext : function(singular, plural, n) {
var translated = Documentation.TRANSLATIONS[singular];
if (typeof translated === 'undefined')
return (n == 1) ? singular : plural;
return translated[Documentation.PLURALEXPR(n)];
},
addTranslations : function(catalog) {
for (var key in catalog.messages)
this.TRANSLATIONS[key] = catalog.messages[key];
this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
this.LOCALE = catalog.locale;
},
/**
* add context elements like header anchor links
*/
addContextElements : function() {
$('div[id] > :header:first').each(function() {
$('<a class="headerlink">\u00B6</a>').
attr('href', '#' + this.id).
attr('title', _('Permalink to this headline')).
appendTo(this);
});
$('dt[id]').each(function() {
$('<a class="headerlink">\u00B6</a>').
attr('href', '#' + this.id).
attr('title', _('Permalink to this definition')).
appendTo(this);
});
},
/**
* workaround a firefox stupidity
* see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
*/
fixFirefoxAnchorBug : function() {
if (document.location.hash && $.browser.mozilla)
window.setTimeout(function() {
document.location.href += '';
}, 10);
},
/**
* highlight the search words provided in the url in the text
*/
highlightSearchWords : function() {
var params = $.getQueryParameters();
var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
if (terms.length) {
var body = $('div.body');
if (!body.length) {
body = $('body');
}
window.setTimeout(function() {
$.each(terms, function() {
body.highlightText(this.toLowerCase(), 'highlighted');
});
}, 10);
$('<p class="highlight-link"><a href="javascript:Documentation.' +
'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
.appendTo($('#searchbox'));
}
},
/**
* init the domain index toggle buttons
*/
initIndexTable : function() {
var togglers = $('img.toggler').click(function() {
var src = $(this).attr('src');
var idnum = $(this).attr('id').substr(7);
$('tr.cg-' + idnum).toggle();
if (src.substr(-9) === 'minus.png')
$(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
else
$(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
}).css('display', '');
if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
togglers.click();
}
},
/**
* helper function to hide the search marks again
*/
hideSearchWords : function() {
$('#searchbox .highlight-link').fadeOut(300);
$('span.highlighted').removeClass('highlighted');
},
/**
* make the url absolute
*/
makeURL : function(relativeURL) {
return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
},
/**
* get the current relative url
*/
getCurrentURL : function() {
var path = document.location.pathname;
var parts = path.split(/\//);
$.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
if (this === '..')
parts.pop();
});
var url = parts.join('/');
return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
},
initOnKeyListeners: function() {
$(document).keydown(function(event) {
var activeElementType = document.activeElement.tagName;
// don't navigate when in search box or textarea
if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT'
&& !event.altKey && !event.ctrlKey && !event.metaKey && !event.shiftKey) {
switch (event.keyCode) {
case 37: // left
var prevHref = $('link[rel="prev"]').prop('href');
if (prevHref) {
window.location.href = prevHref;
return false;
}
case 39: // right
var nextHref = $('link[rel="next"]').prop('href');
if (nextHref) {
window.location.href = nextHref;
return false;
}
}
}
});
}
};
// quick alias for translations
_ = Documentation.gettext;
$(document).ready(function() {
Documentation.init();
});
docs/_build/html/_static/custom.css deleted 100644 → 0
/* This file intentionally left blank. */
docs/_build/html/_static/documentation_options.js
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '1.3.0',
LANGUAGE: 'None',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
FILE_SUFFIX: '.html',
LINK_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt',
NAVIGATION_WITH_KEYS: false
NAVIGATION_WITH_KEYS: false,
SHOW_SEARCH_SUMMARY: true,
ENABLE_SEARCH_SHORTCUTS: true,
};
\ No newline at end of file
docs/_build/html/_static/jquery-3.4.1.js deleted 100644 → 0
This source diff could not be displayed because it is too large. You can view the blob instead.
docs/_build/html/_static/jquery.js
This source diff could not be displayed because it is too large. You can view the blob instead.
docs/_build/html/_static/language_data.js
......@@ -5,15 +5,16 @@
* This script contains the language-specific data used by searchtools.js,
* namely the list of stopwords, stemmer, scorer and splitter.
*
* :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
* :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
/* Non-minified version JS is _stemmer.js if file is provided */
/* Non-minified version is copied as a separate JS file, is available */
/**
* Porter Stemmer
*/
......@@ -196,102 +197,3 @@ var Stemmer = function() {
}
}
var splitChars = (function() {
var result = {};
var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
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return result;
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var start = -1;
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docs/_build/analysis.html → docs/_build/html/analysis.html
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" />
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Analyzing the ESGEMME output &mdash; esgemme 1.3.0 documentation</title><link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<title>Analyzing the ESGEMME output &mdash; esgemme 1.3.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
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<script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
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<link rel="next" title="Preparing Your Own Input" href="input-preparation.html" />
<link rel="prev" title="Using ESGEMME via Docker" href="docker.html" />
</head>
......@@ -38,10 +42,12 @@
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption"><span class="caption-text">Contents:</span></p>
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESGEMME via Docker</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Analyzing the ESGEMME output</a></li>
<li class="toctree-l1"><a class="reference internal" href="input-preparation.html">Preparing Your Own Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
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......@@ -68,8 +74,8 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="analyzing-the-esgemme-output">
<h1>Analyzing the ESGEMME output<a class="headerlink" href="#analyzing-the-esgemme-output" title="Permalink to this headline"></a></h1>
<section id="analyzing-the-esgemme-output">
<h1>Analyzing the ESGEMME output<a class="headerlink" href="#analyzing-the-esgemme-output" title="Permalink to this heading"></a></h1>
<p>By default, ESGEMME will output the following files: *
myProt_normPred_evolEpi.txt * myProt_normPred_evolInd.txt *
myProt_normPred_evolCombi.txt</p>
......@@ -80,13 +86,14 @@ query sequence. If the user provides her/his own list of mutations, then
only the global epistatic model will be run and the output file will
contain 2 columns, the first one with the mutations, the second one with
the normalized predicted effects.</p>
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<section id="preparing-your-input-msa-and-pdb-with-colabfold">
<h2>Preparing Your Input MSA and PDB with Colabfold<a class="headerlink" href="#preparing-your-input-msa-and-pdb-with-colabfold" title="Permalink to this heading"></a></h2>
<p>You have a fasta file for your protein of interest and you want to understand
impact of (certain) mutations.
Before starting, please make sure that your fasta file does not contain a gap.
The quickest method to obtain both multiple sequence alignment and a protein
structure is to use Colabfold. Let’s do this step by step:</p>
<ol class="arabic">
<li><p>Let’s go the Colabfold web site:</p>
<p><a class="reference external" href="https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb">https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb</a></p>
<p>Sign in using your gmail account.</p>
</li>
<li><p>Click on the ‘Connect’ button on the top right hand side.</p></li>
<li><p>Clean ‘query_sequence’ box and paste your sequence to the ‘query_sequence’ box.
For me, I selected adenylate kinase (AKE) as my example fasta sequence
(<a class="reference external" href="https://www.rcsb.org/fasta/entry/4AKE/display">https://www.rcsb.org/fasta/entry/4AKE/display</a>).</p></li>
<li><p>Change the ‘jobname’ to something that makes more sense to you.</p></li>
<li><p>Go to the menu bar of your ‘AlphaFold2.ipynb’ notebook, where ‘File, Edit,
View, Insert, Runtime, Tools, Help’ are listed. Click on the Runtime and
select ‘Run all’.</p></li>
<li><p>This process make take from a few minutes to a few hours depending on your
protein size. It will give you an a3m file and up to 5 PDB models. Put these
files in a clean folder and change the directory to that folder in your
terminal.</p></li>
<li><p>Unfortunately, a3m file is not in fasta format and it contains gap columns.
We have to clean those gaps. We can do that with a GUI program like Ugene
or Jalview. However, it is a labor intensive procedure. Here, I will use a
small tool that I developed and added to the ESGEMME docker image that I created.</p></li>
<li><p>Start the docker image with the following command:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo<span class="w"> </span>docker<span class="w"> </span>run<span class="w"> </span>-ti<span class="w"> </span>--rm<span class="w"> </span>--mount<span class="w"> </span><span class="nv">type</span><span class="o">=</span>bind,source<span class="o">=</span><span class="nv">$PWD</span>,target<span class="o">=</span>/home/tekpinar/research/myexample<span class="w"> </span><span class="se">\</span>
tekpinar/esgemme-docker:v1.3.0
</pre></div>
</div>
</li>
<li><p>Now, change the directory to myexample folder.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span><span class="w"> </span>../myexample/
ls<span class="w"> </span>-l
</pre></div>
</div>
<p>We are supposed to see our a3m and pdb files in this folder.</p>
</li>
<li><p>Let’s use a small script from hhsuite to convert a3m file to fasta format.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>reformat.pl<span class="w"> </span>a3m<span class="w"> </span>fas<span class="w"> </span>AKE.a3m<span class="w"> </span>AKE.fasta
</pre></div>
</div>
</li>
<li><p>Final step and we are there:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>demust<span class="w"> </span>removegaps<span class="w"> </span>-i<span class="w"> </span>AKE.fasta<span class="w"> </span>-o<span class="w"> </span>AKE_nogaps.fasta
</pre></div>
</div>
</li>
</ol>
<p>Congratulations! Now, you have all the input files required for ESGEMME:
I. An input MSA: AKE_nogaps.fasta
II. An input PDB: myprotein.pdb</p>
</section>
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<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing the ESGEMME output</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#installing-the-dependencies">Installing the dependencies:</a></li>
<li class="toctree-l2"><a class="reference internal" href="#getting-the-source-code-and-preparing-the-environment">Getting the source code and preparing the environment:</a></li>
......@@ -74,45 +78,51 @@
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<div class="section" id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline"></a></h1>
<section id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this heading"></a></h1>
<p>ESGEMME is implemented in Python 3 and R. It has been tested only on
Linux. Since ESGEMME has many dependencies, we recommend using our web
site or our docker image. If you are a determined user, here comes the
steps required to install it from the source.</p>
<div class="section" id="installing-the-dependencies">
<h2>Installing the dependencies:<a class="headerlink" href="#installing-the-dependencies" title="Permalink to this headline"></a></h2>
<p>ESGEMME has the following external dependencies: * Joint Evolutionary
Trees: <a class="reference external" href="http://www.lcqb.upmc.fr/JET2/">http://www.lcqb.upmc.fr/JET2/</a> and its dependencies: - naccess:
<a class="reference external" href="http://www.bioinf.manchester.ac.uk/naccess/">http://www.bioinf.manchester.ac.uk/naccess/</a> - muscle:
<a class="reference external" href="https://www.drive5.com/muscle/">https://www.drive5.com/muscle/</a> ** * seqinr R package:
<a class="reference external" href="https://cran.r-project.org/web/packages/seqinr/index.html">https://cran.r-project.org/web/packages/seqinr/index.html</a> * dssp for
secondary structure prediction.</p>
<section id="installing-the-dependencies">
<h2>Installing the dependencies:<a class="headerlink" href="#installing-the-dependencies" title="Permalink to this heading"></a></h2>
<p>ESGEMME has the following external dependencies:</p>
<ul class="simple">
<li><p>Joint Evolutionary Trees: <a class="reference external" href="http://www.lcqb.upmc.fr/JET2/">http://www.lcqb.upmc.fr/JET2/</a> and its dependencies:</p>
<ul>
<li><p>java</p></li>
<li><p>naccess: <a class="reference external" href="http://www.bioinf.manchester.ac.uk/naccess/">http://www.bioinf.manchester.ac.uk/naccess/</a></p></li>
<li><p>muscle: <a class="reference external" href="https://www.drive5.com/muscle/">https://www.drive5.com/muscle/</a></p></li>
</ul>
</li>
<li><p>seqinr R package: <a class="reference external" href="https://cran.r-project.org/web/packages/seqinr/index.html">https://cran.r-project.org/web/packages/seqinr/index.html</a></p></li>
<li><p>dssp for secondary structure prediction.</p></li>
</ul>
<p>These tools should be installed to be able to use ESGEMME.</p>
</div>
<div class="section" id="getting-the-source-code-and-preparing-the-environment">
<h2>Getting the source code and preparing the environment:<a class="headerlink" href="#getting-the-source-code-and-preparing-the-environment" title="Permalink to this headline"></a></h2>
</section>
<section id="getting-the-source-code-and-preparing-the-environment">
<h2>Getting the source code and preparing the environment:<a class="headerlink" href="#getting-the-source-code-and-preparing-the-environment" title="Permalink to this heading"></a></h2>
<p>Download the ESGEMME source code from
<a class="reference external" href="http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME">http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME</a>. Define and export the
environment variable ESGEMME_PATH=/path-to-ESGEMME-directory/</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">ESGEMME_PATH</span><span class="o">=</span>/path-to-ESGEMME-directory/
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">ESGEMME_PATH</span><span class="o">=</span>/path-to-ESGEMME-directory/
</pre></div>
</div>
</div>
<div class="section" id="configuring-default-conf-file">
<h2>Configuring default.conf file<a class="headerlink" href="#configuring-default-conf-file" title="Permalink to this headline"></a></h2>
</section>
<section id="configuring-default-conf-file">
<h2>Configuring default.conf file<a class="headerlink" href="#configuring-default-conf-file" title="Permalink to this heading"></a></h2>
<p>Inside ESGEMME folder, there is an important file called default.conf.
This file contains essential parameters of ESGEMME, such as paths of
external parts, default internal parameters. etc. You have to correct the Software section of this
file according to your system.</p>
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