Louis BECQUEY / biorseo

Go to a project
Toggle navigation Toggle navigation pinning
Louis BECQUEY
e748c210 1 parent d3523f97

data restructuration

Expand all
Inline Side-by-side
Showing 17 changed files with 37 additions and 60 deletions
......@@ -23,5 +23,11 @@ results/*
log_of_the_run.sh
logBadDesc.txt
gurobi.log
IL*
HL*
temp/*
# data
data/modules/BGSU/HL/3.2/diagnostic/*
data/modules/BGSU/HL/3.2/lib/*
data/modules/BGSU/IL/3.2/diagnostic/*
data/modules/BGSU/IL/3.2/lib/*
data/modules/DESC/*.desc
\ No newline at end of file
......
......@@ -2,9 +2,6 @@
CPLEXDir="/opt/ibm/ILOG/CPLEX_Studio128_Student"
IEIGEN="/usr/local/include/eigen3"
INUPACK="/usr/local/include/nupack"
biorseoDir="/nhome/siniac/lbecquey/Software/biorseo"
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="/local/local/labo/03_tests_biominserter/No_Redondance_DESC/"
bypdir="/nhome/siniac/lbecquey/Software/BayesPairing/bayespairing/src"
biorseoDir="/nhome/siniac/lbecquey/Software/biorseo"
\ No newline at end of file
bypdir="/nhome/siniac/lbecquey/Software/BayesPairing/bayespairing/src"
\ No newline at end of file
......
Biorseo (Bi-Objective RNA Structure Efficient Optimizer)
===================================
This tool predicts the secondary structure of a RNA sequence with pieces of 3D information (non-canonical contacts) at some places,
by identifying zones that can fold like known modules from data like the RNA 3D Motif Atlas or Rna3Dmotifs.
......@@ -47,13 +49,16 @@ OBJECTIVE FUNCTIONS FOR THE MODULE INSERTION CRITERIA
* Benchmarks show Biorseo does not perform better than simpler tools like RNAsubopt alone. Please use RNAsubopt (ViennaRNA package) or Fold (RNAstructure package).
- 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.
* 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.
* 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 `
* 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`
4/ Installation
==================================
DEPENDENCIES
### 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.
......@@ -79,13 +84,13 @@ make -j4
sudo make install
```
OPTIONAL DEPENDENCIES FOR USE OF JAR3D
### 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
### 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 :
......@@ -95,15 +100,16 @@ cd BayesPairing
pip install .
```
RNA3DMOTIFS DATA
### 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). 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)).
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
### 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.
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
### 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"
......@@ -118,4 +124,11 @@ BUILDING
* Build it: `make -j4`
* The working executable file is `./bin/biorseo`.
BAYESPAIRING USERS: PREPARE BAYESIAN NETWORKS
\ No newline at end of file
### 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.
......
>E.coli_alpha_operon_mRNA
UGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGA
(((((((.(((((........[[[[....[[[[....{{{{.))))))))))))..........................]]]].....]]]]...........}}}}
\ No newline at end of file
>E.coli_alpha_operon_mRNA
UGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGA
E.coli_alpha_operon_mRNA
UGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGA
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZE.A.89 + 3IZF.A.191 + 3PYO.A.85 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZE.A.89 + 3IZF.A.191 + 3PYO.A.85 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZE.A.89 + 3IZF.A.191 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 + 3PYO.A.85 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 + 3PYO.A.85 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZE.A.89 + 3IZF.A.191 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 450.0000000 24.6634106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZE.A.89 + 3IZF.A.191 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 + 3PYO.A.85 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZE.A.89 + 3IZF.A.191 + 3PYO.A.85 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZE.A.89 + 3IZF.A.191 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 475.0000000 24.6241106
((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 + 3PYO.A.85 475.0000000 24.6241106
(((((((.(((((........[[[[....[[[[....{{{{.))))))))))))..........................]]]].....]]]]...........}}}}
This diff is collapsed. Click to expand it.
This diff is collapsed. Click to expand it.
......@@ -15,15 +15,15 @@ import ast
# Retrieve Paths from file EditMe
jar3dexec = ""
HLmotifDir = ""
ILmotifDir = ""
descfolder = ""
bypdir = ""
biorseoDir = "."
exec(compile(open(biorseoDir+"/EditMe").read(), '', 'exec'))
runDir = path.dirname(path.realpath(__file__))
dataFile = argv[1]
outputDir = biorseoDir + "/results/"
HLmotifDir = biorseoDir + "/data/modules/BGSU/HL/3.2/lib"
ILmotifDir = biorseoDir + "/data/modules/BGSU/IL/3.2/lib"
descfolder = biorseoDir + "/data/modules/DESC"
# Create some folders to store the results
subprocess.call(["mkdir", "-p", outputDir])
......