Louis BECQUEY / biorseo

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Louis BECQUEY
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Cosmetics & doc update

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......@@ -13,6 +13,7 @@ doc/*.fdb_latexmk
# Compiled Object files
obj/*
doc/*.pdf
# Executables
bin/*
......
Installation
==================================
### CLONING
* Clone this git repository : `git clone https://github.com/persalteas/biorseo.git` and `cd biorseo`.
* Create folders for the modules you will use: `mkdir -p data/modules/`. If you plan to use several module sources, add subdirectories : `mkdir -p data/modules/DESC` and `mkdir -p data/modules/BGSU`
### RNA3DMOTIFS DATA
If you use Rna3Dmotifs, you need to get RNA-MoIP's .DESC dataset: download it from [GitHub](https://github.com/McGill-CSB/RNAMoIP/blob/master/CATALOGUE.tgz). Put all the .desc from the `Non_Redundant_DESC` folder into `./data/modules/DESC`. Otherwise, you also can run Rna3Dmotifs' `catalog` program to get your own DESC modules collection from updated 3D data (download [Rna3Dmotifs](https://rna3dmotif.lri.fr/Rna3Dmotif.tgz)). You also need to move the final DESC files into `./data/modules/DESC`.
### THE RNA 3D MOTIF ATLAS DATA
If not done during the installation of JAR3D, get the latest version of the HL and IL module models from the [BGSU website](http://rna.bgsu.edu/data/jar3d/models/) and extract the Zip files. Put the HL and IL folders from inside the Zip files into `./data/modules/BGSU`. Note that only the latest Zip is required.
### DEPENDENCIES
- Make sure you have Python 3.5+, Cmake, and a C++ compiler installed on your distribution. Please, it's 2019, use a recent one, we use the 2017 C++ standard. The compilation will not work with Ubuntu 16's GCC 5.4 for example. Tested with libstdc++-dev >= 6.0, so use GCC >=6.0 or Clang >= 6.0.
- Install automake, libboost-program-options and libboost-filesystem.
- Download and install [IBM ILOG Cplex optimization studio](https://www.ibm.com/analytics/cplex-optimizer), an academic account is required. The free version is too limited, you must register as academic. This is also free.
- Download and install Eigen: Get the latest Eigen archive from http://eigen.tuxfamily.org. Unpack it, and install it.
```bash
wget http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz -O eigen_src.tar.gz
tar -xf eigen_src.tar.gz
cd eigen-eigen-323c052e1731
mkdir build
cd build
cmake ..
sudo make install
```
- Download and install NUPACK: Register on [Nupack's website](http://www.nupack.org/downloads/source), download the source, unpack it, build it, and install it:
```bash
wget http://www.nupack.org/downloads/serve_file/nupack3.2.2.tar.gz
tar -xf nupack3.2.2.tar.gz
cd nupack3.2.2
mkdir build
cd build
cmake ..
make -j4
sudo make install
```
You will notice that the installation process is not complete, some of the headers are not well copied to /usr/local. Solve it manually:
```
sudo cp nupack3.2.2/src/thermo/*.h /usr/local/include/nupack/thermo/
```
### OPTIONAL DEPENDENCIES FOR USE OF JAR3D
- Download and install RNAsubopt from the [ViennaRNA package](https://www.tbi.univie.ac.at/RNA/).
- Download and install Java runtime (Tested with Java 10)
- Download the latest JAR3D executable "*jar3d_releasedate.jar*" from [the BGSU website](http://rna.bgsu.edu/data/jar3d/models/).
### OPTIONAL DEPENDENCIES FOR USE OF BAYESPAIRING
- Download and install RNAfold from the [ViennaRNA package](https://www.tbi.univie.ac.at/RNA/) (if not already done at the previous step).
- Make sure you have Python 3.5+ with packages networkx, numpy, regex, wrapt and biopython. You can install them with pip, you will need the python3-dev package to build them.
- Clone the latest BayesPairing Git repo, and install it :
```
git clone http://jwgitlab.cs.mcgill.ca/sarrazin/rnabayespairing.git BayesPairing
cd BayesPairing
pip install .
```
### BUILDING
* Edit the file `EditMe` to set the paths of the above dependencies and data. Fields that you will not use can be ignored (ex: bypdir if you do not use BayesPairing). Example of my setup:
* CPLEXDir="/opt/ibm/ILOG/CPLEX_Studio128_Student"
* IEIGEN="/usr/local/include/eigen3"
* INUPACK="/usr/local/include/nupack"
* jar3dexec="/nhome/siniac/lbecquey/Software/jar3dbin/jar3d_2014-12-11.jar"
* bypdir="/nhome/siniac/lbecquey/Software/BayesPairing/bayespairing/src"
* biorseoDir="/nhome/siniac/lbecquey/Software/biorseo"
* You might want to edit `Makefile` if you are not using clang as compiler. For example, if you use g++, replace clang++ by g++.
* Build it: `make -j4`
* Check if the executable file exists: `./bin/biorseo --version`.
### BAYESPAIRING USERS: PREPARE BAYESIAN NETWORKS
We run an example job for it to build the bayesian networks of our modules.
```
cd rnabayespairing/src
python3 parse_sequences.py -d rna3dmotif -seq ACACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACACCGCCGAGGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAACGAGACGUUAAGCCCACGAGCACUAACAGACCAAAGCCAUCAU -ss ".................................................................((...............)xxxx(...................................................)xxx).............."
```
Use `-d rna3dmotif` or `-d 3dmotifatlas` depending on the module source you are planning to use.
This is a quite long step, but the bayesian networks will be ready for all the future uses.
......@@ -37,6 +37,7 @@ $(OBJECTS): $(OBJDIR)/%.o : $(SRCDIR)/%.cpp $(INCLUDES)
@echo "\033[00;32mCompiled "$<".\033[00m"
doc: mainpdf supppdf
@echo "\033[00;32mLaTeX documentation rendered.\033[00m"
mainpdf: doc/main_bioinformatics.tex doc/references.bib doc/bioinfo.cls doc/natbib.bst
cd doc; pdflatex -synctex=1 -interaction=nonstopmode -file-line-error main_bioinformatics
......
......@@ -50,85 +50,45 @@ OBJECTIVE FUNCTIONS FOR THE MODULE INSERTION CRITERIA
- If you **might expect a pseudoknot, or don't know**:
* The most promising method is the use of direct pattern matching with Rna3Dmotifs and function B. But this method is sometimes subject to combinatorial explosion issues. If you have a long RNA or a large number of loops, don't use it. Example:
`./bin/biorseo -s PDB_00304.fa --descfolder ./data/modules/DESC --type B -o PDB_00304.rawB `
`./biorseo.py -i PDB_00304.fa --rna3dmotifs --patternmatch --func B`
* The use of the RNA 3D Motif Atlas placed by JAR3D and scored with function B is not subject to combinatorial issues, but performs a bit worse. It also returns less solutions. Example:
`./bin/biorseo -s PDB_00304.fa --jar3dcsv PDB_00304.sites.csv --type B -o PDB_00304.jar3dB`
`./bin/biorseo -i PDB_00304.fa --3dmotifatlas --jar3d --func B`
4/ Installation
==================================
### DEPENDENCIES
- Make sure you have Python 3.5+, Cmake, and a C++ compiler installed on your distribution.
- Install automake and libboost-filesystem.
- Download and install [IBM ILOG Cplex optimization studio](https://www.ibm.com/analytics/cplex-optimizer), an academic account is required. The free version is too limited, you must register as academic. This is also free.
- Download and install Eigen: Get the latest Eigen archive from http://eigen.tuxfamily.org. Unpack it, and install it.
```bash
wget http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz -O eigen_src.tar.gz
tar -xf eigen_src.tar.gz
cd eigen-eigen-323c052e1731
mkdir build
cd build
cmake ..
sudo make install
```
- Download and install NUPACK: Register on [Nupack's website](http://www.nupack.org/downloads/source), download the source, unpack it, build it, and install it:
```bash
wget http://www.nupack.org/downloads/serve_file/nupack3.2.2.tar.gz
tar -xf nupack3.2.2.tar.gz
cd nupack3.2.2
mkdir build
cd build
cmake ..
make -j4
sudo make install
```
### OPTIONAL DEPENDENCIES FOR USE OF JAR3D
- Download and install RNAsubopt from the [ViennaRNA package](https://www.tbi.univie.ac.at/RNA/).
- Download and install Java runtime (Tested with Java 10)
- Download the latest JAR3D executable "*jar3d_releasedate.jar*", and latest IL and HL models from [here](http://rna.bgsu.edu/data/jar3d/models/).
Note that only the latest version is required (not all the versions provided in the folders).
### OPTIONAL DEPENDENCIES FOR USE OF BAYESPAIRING
- Download and install RNAfold from the [ViennaRNA package](https://www.tbi.univie.ac.at/RNA/).
- Make sure you have Python 3.5+ with packages networkx, numpy, regex, wrapt and biopython
- Clone the latest BayesPairing Git repo, and install it :
```
git clone http://jwgitlab.cs.mcgill.ca/sarrazin/rnabayespairing.git BayesPairing
cd BayesPairing
pip install .
```
Check the file INSTALL.md for installation instructions.
### RNA3DMOTIFS DATA
If you use Rna3Dmotifs, you need to get RNA-MoIP's .DESC dataset: download it from [GitHub](https://github.com/McGill-CSB/RNAMoIP/blob/master/CATALOGUE.tgz). Put all the .desc from the `Non_Redundant_DESC` folder into `./data/modules/DESC`. Otherwise, you also can run Rna3Dmotifs' `catalog` program to get your own DESC modules collection from updated 3D data (download [Rna3Dmotifs](https://rna3dmotif.lri.fr/Rna3Dmotif.tgz)). You also need to move the final DESC files into `./data/modules/DESC`.
### THE RNA 3D MOTIF ATLAS DATA
If not done during the installation of JAR3D, get the latest version of the HL and IL module models from the [BGSU website](http://rna.bgsu.edu/data/jar3d/models/) and extract the Zip files. Put the HL and IL folders into `./data/modules/BGSU`.
### BUILDING
* Clone this git repository : `git clone https://github.com/persalteas/biorseo.git` and `cd biorseo`.
* Edit the file `EditMe` to set the paths of the above dependencies and data. Fileds that you will not use can be ignored (ex: bypdir if you do not use BayesPairing). Example of my setup:
* CPLEXDir="/opt/ibm/ILOG/CPLEX_Studio128_Student"
* IEIGEN="/usr/local/include/eigen3"
* INUPACK="/usr/local/include/nupack"
* jar3dexec="/nhome/siniac/lbecquey/Software/jar3dbin/jar3d_2014-12-11.jar"
* ILmotifDir="/nhome/siniac/lbecquey/Data/RNA/motifs/BGSU/Matlab_results/IL/3.2/lib"
* HLmotifDir="/nhome/siniac/lbecquey/Data/RNA/motifs/BGSU/Matlab_results/HL/3.2/lib"
* descfolder="/nhome/siniac/lbecquey/Data/RNA/motifs/Rna3Dmotifs/No_Redondance_DESC/"
* bypdir="/nhome/siniac/lbecquey/Software/BayesPairing/bayespairing/src"
* biorseoDir="/nhome/siniac/lbecquey/Software/biorseo"
* You might want to edit `Makefile` if you are not using clang as compiler. For example, if you use g++, replace clang++ by g++.
* Build it: `make -j4`
* The working executable file is `./bin/biorseo`.
### BAYESPAIRING USERS: PREPARE BAYESIAN NETWORKS
We run an example job for it to build the bayesian networks of our modules.
5/ List of Options
==================================
```
cd rnabayespairing/src
python3 parse_sequences.py -d rna3dmotif -seq ACACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACACCGCCGAGGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAACGAGACGUUAAGCCCACGAGCACUAACAGACCAAAGCCAUCAU -ss ".................................................................((...............)xxxx(...................................................)xxx).............."
-h [ --help ] Print this help message
--version Print the program version
-i [ --seq=… ] FASTA file with the query RNA sequence
-p [ --patternmatch ] Use regular expressions to place modules in the sequence
-j [ --jar3d ] Use JAR3D to place modules in the sequence (requires --3dmotifatlas)
-b [ --bayespairing ] Use BayesPairing to place modules in the sequence
-o [ --output=… ] Folder where to output files
-f [ --func=… ] (A, B, C or D, default is B) Objective function to score module insertions:
(A) insert big modules (B) insert light, high-order modules
(c) insert modules which score well with the sequence
(D) insert light, high-order modules which score well with the sequence.
C and D require cannot be used with --patternmatch.
-c [ --first-objective=… ] (default 1) Objective to solve in the mono-objective portions of the algorithm.
(1) is the module objective given by --func, (2) is the expected accuracy of the structure.
-l [ --limit=… ] (default 500) Intermediate number of solutions in the Pareto set from whichwe give up the computation.
-t [ --theta=… ] (default 0.001) Pairing-probability threshold to consider or not the possibility of pairing
-n [ --disable-pseudoknots ] Add constraints to explicitly forbid the formation of pseudoknots
-v [ --verbose ] Print what is happening to stdout
--modules-path=… Path to the modules data.
The folder should contain modules in the DESC format as output by Djelloul & Denise's
'catalog' program for use with --rna3dmotifs, or should contain the IL/ and HL/ folders from a release of
the RNA 3D Motif Atlasfor use with --3dmotifatlas.
Consider placing these files on a fast I/O device (NVMe SSD, ...)
Examples:
biorseo.py -i myRNA.fa -o myResultsFolder/ --rna3dmotifs --patternmatch --func B
biorseo.py -i myRNA.fa -o myResultsFolder/ --3dmotifatlas --jar3d --func B -l 800
biorseo.py -i myRNA.fa --3dmotifatlas --bayespairing --func D
```
Use `-d rna3dmotif` or `-d 3dmotifatlas` depending on the module source you are planning to use.
This is a quite long step, but the bayesian networks will be ready for all the future uses.
......