removed stuff from biorseo

-results_*
-build_BiORSEO_docker_image_ubuntu18.sh
-deploy_BiORSEO_docker_image_linux.sh
-INSTALL.md
-Readme.md
-benchmark_results/
-doc/

-FROM ubuntu:bionic
-
-# installing dependencies
-RUN apt-get update -yq && \
-    apt-get upgrade -y && \
-    apt-get install -y python3-dev python3-pip openjdk-11-jre libgsl23 libgslcblas0 libboost-program-options-dev libboost-filesystem-dev && \
-    rm -rf /var/lib/apt/lists/*
-
-# compiled biorseo
-COPY . /biorseo 
-# ViennaRNA installer
-ADD "https://www.tbi.univie.ac.at/RNA/download/ubuntu/ubuntu_18_04/viennarna_2.4.14-1_amd64.deb" /
-# jar3d archive
-ADD http://rna.bgsu.edu/data/jar3d/models/jar3d_2014-12-11.jar /
-
-# install codes
-RUN dpkg -i /viennarna_2.4.14-1_amd64.deb && \
-    apt-get install -f          && \
-    \
-    pip3 install networkx numpy regex wrapt biopython /biorseo/BayesPairing && \
-    \
-    cd / && \
-    rm -rf /biorseo/BayesPairing /ViennaRNA-2.4.13 /ViennaRNA-2.4.13.tar.gz
-WORKDIR /biorseo
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-#!/usr/bin/python3
-
-# This script's purpose is to extract information about the CaRNAval
-# RINS from a Python pickle object containing RINs from their RIN.py class.
-# We do this because the official JSON file is hard to understand, and Antoine Soulé
-# recommended the pickle.
-
-import networkx, os, pickle, subprocess, sys
-
-if __name__=="__main__":
-
-    
-    rin_DIR = os.getcwd() + "/../data/modules/RIN/"
-    filename = "CaRNAval_1_as_dictionnary.nxpickled"
-
-    # Check that we can find CaRNAval RINs, and load the dataset
-    try:
-        sys.path.append(os.path.abspath(rin_DIR))
-        import RIN
-    except ImportError:
-        # We have to download it
-        subprocess.run(["wget", '-O', '../data/modules/carnaval_dataset.zip', "http://carnaval.lri.fr/carnaval_dataset.zip"])
-        subprocess.run(["unzip", '-ou', '../data/modules/carnaval_dataset.zip', "carnaval_dataset/CaRNAval_1_as_dictionnary.nxpickled", "carnaval_dataset/RIN.py"])
-        subprocess.run(["rm", "-f", "../data/modules/RIN/", "../data/modules/carnaval_dataset.zip"])
-        subprocess.run(["mv", "carnaval_dataset/", "../data/modules/RIN/"])
-        sys.path.append(os.path.abspath(rin_DIR))
-        import RIN
-
-    try:
-        objects = []
-        with (open(rin_DIR+filename, "rb")) as openfile:
-            while True:
-                try:
-                    objects.append(pickle.load(openfile))
-                except EOFError:
-                    break
-        print("Dataset loaded")
-    except OSError:
-        print("File not found : " + rin_DIR + filename)
-        exit(1)
-
-    # Creation of a directory to extract RINs from the pickle file to individual files
-    try:
-        os.makedirs(rin_DIR + "Subfiles", exist_ok=True)
-    except OSError:
-        print("Creation of the directory %s failed" % (rin_DIR + "Subfiles"))
-        exit(1)
-
-    # Loop on every CaRNAval module and extract it from the Python object to flat text file
-    n_modules = len(objects[0]) # ? to
-    for i in range(1,1+n_modules):
-        motif = objects[0][i].graph
-        f = open(rin_DIR + "Subfiles/" + str(i-1) + ".txt", "w+")
-        f.write("ntA,ntB,long_range;...\n")
-
-        components = []
-        comp = []
-        nodes = list(motif)
-        nodes.sort()
-        for node in nodes:
-            if comp == []:
-                comp.append(node)
-            else:
-                if comp[-1] + 1 != node : #not the same component
-                    components.append(comp)
-                    comp = []
-                    comp.append(node)
-                else :
-                    comp.append(node)
-        components.append(comp)
-
-        #print(nodes)
-
-        basepairs = ""
-        edges = list(motif.edges())
-        for a in edges:
-            if motif.edges[a]['label'] == 'CWW' :
-                ntA = nodes.index(a[0])
-                ntB = nodes.index(a[1])
-
-                if ntA <= ntB :
-                    basepairs += str(ntA) + "," + str(ntB) + "," + str(motif.edges[a]['long_range']) + ";"
-
-        f.write(basepairs + "\n")
-        f.write("pos;k;seq\n")
-
-        num_nt = -1
-        for a in components:
-            seq = ""
-            data_comp = str(num_nt+1)
-            for b in a:
-                num_nt += 1
-
-                # sometimes in the nxpicled file, a node has the attribute "realnt", 
-                # and sometimes "real_nt", but it's the same thing
-                try:
-                    seq += motif.nodes[b]["realnt"]
-                except:
-                    seq += motif.nodes[b]["real_nt"]
-            data_comp += "," + str(num_nt) + ";" + str(len(a)) + ";" + seq + "\n"
-            f.write(data_comp)
-
-        f.close()
-        # print(str(i-1) + ".txt created")
-
-    print("Successfully parsed "+filename, ", now individual RINs are saved in Subfiles/ folder.", sep='')
-

-# ============================ IMPORTS ====================================
-import subprocess
-import time
-import resource
-
-# take a RNA sequence and cut it from 100 bases to actual length
-# then measure computation time, peak memory, and number of solutions for each length
-
-# This RNA is actually a 16S rRNA from PDB 1J5E.
-# http://ndbserver.rutgers.edu/service/ndb/atlas/summary
-seq = "UUUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU"
-
-step = 100
-n = len(seq)
-
-while step < len(seq)+50:
-	sub_seq = seq[0:(min(step,n))]
-
-	# write the sequence to file
-	fasta = open("data/fasta/ZDFS33.fa", 'w')
-	fasta.write(">__'ZDFS33 : 0-" + str(len(sub_seq)) + "'\n" + sub_seq)
-	fasta.close()
-
-	# run biorseo on it, with default options
-	cmd = ["./bin/biorseo", "-d", "./data/modules/DESC", "-s", "./ZDFS33.fa", "-v"]
-	old_time = time.time()
-	output = subprocess.check_output(cmd, stderr=subprocess.DEVNULL).decode("utf-8").split("\n")[-5:]
-	run_time = time.time() - old_time
-	max_ram = resource.getrusage(resource.RUSAGE_CHILDREN).ru_maxrss
-
-	for line in output :
-		if "Quitting because combinatorial issues" in line :
-			nb_sol = -1
-		elif "solutions kept" in line :
-			nb_sol = line.split(",")[1].split()[0]
-
-	print(len(sub_seq), "first nucleotides :", nb_sol, "solutions in", run_time, "seconds, using", max_ram, "kb of RAM")
-
-	step += 50

-#!/bin/bash
-
-echo "WARNING: The purpose of this file is to document how the docker image was built.";
-echo "You cannot execute it directly, because of licensing reasons. Please get your own:";
-echo "- CPLEX academic version: cplex_installer_12.8_Student.bin";
-echo "- Nupack header files: nupack_3.2.2.tar.gz";
-exit 0;
-
-cd ../
-THISDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-
-####################################################### Dependencies ##############################################################
-sudo apt install -y clang-7 cmake make automake libboost-program-options-dev libboost-filesystem-dev openjdk-11-jre
-sudo update-alternatives --install /usr/bin/clang++ clang++ /usr/bin/clang++-7 100
-sudo update-alternatives --install /usr/bin/clang clang /usr/bin/clang-7 100
-
-# CPLEX: only to build biorseo
-# HERE YOU SHOULD GET YOUR OWN cplex_installer_12.8_Student.bin ! I am not allowed to share mine anymore.
-chmod +x cplex_installer_12.8_Student.bin
-printf "4\n\n1\n\n\n\n\n" | sudo ./cplex_installer_12.8_Student.bin
-rm cplex_installer_12.8_Student.bin
-
-# Eigen: only to build biorseo (no need to give it to the docker image)
-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
-cd ../..
-rm -rf eigen_src.tar.gz eigen-eigen-323c052e1731
-
-# Nupack: only to build biorseo (no need to give it to the docker image)
-#curl -u yourname@yourUni.com:yourPassword http://www.nupack.org/downloads/serve_file/nupack3.2.2.tar.gz --output nupack3.2.2.tar.gz
-tar -xf nupack3.2.2.tar.gz
-cd nupack3.2.2
-mkdir build
-cd build
-cmake ..
-make -j8
-sudo make install
-cd ../..
-sudo cp nupack3.2.2/src/thermo/*.h /usr/local/include/nupack/thermo/
-rm -rf nupack3.2.2.tar.gz nupack3.2.2/
-
-# BayesPairing: install on the docker image (done by the Dockerfile)
-git clone http://jwgitlab.cs.mcgill.ca/sarrazin/rnabayespairing.git BayesPairing
-
-######################################################### Build Biorseo ###########################################################
-# build here, install later on the docker image (done by the Dockerfile)
-mkdir -p results
-make -j 8
-make clean
-rm -rf doc/ obj/
-
-######################################################## Build Docker container ##################################################
-# Execute the Dockerfile and build the image
-docker build . -t biorseo

-
-#!/bin/bash
-######################################################## RNA modules ##############################################################
-
-cd ../
-
-# Rna3Dmotifs data
-mkdir -p data/modules/DESC
-wget https://github.com/McGill-CSB/RNAMoIP/raw/master/CATALOGUE.tgz
-tar -xvzf CATALOGUE.tgz 
-mv No_Redondance_DESC/*.desc data/modules/DESC/
-rm -r No_Redondance_VIEW3D No_Redondance_DESC CATALOGUE.tgz
-
-# The RNA 3D Motif Atlas
-mkdir -p data/modules/BGSU
-wget http://rna.bgsu.edu/data/jar3d/models/HL/HL_3.2_models.zip
-unzip HL_3.2_models.zip
-mv HL data/modules/BGSU
-rm HL_3.2_models.zip
-wget http://rna.bgsu.edu/data/jar3d/models/IL/IL_3.2_models.zip
-unzip IL_3.2_models.zip
-mv IL data/modules/BGSU
-rm IL_3.2_models.zip
-
-# Install BayesPairing
-sudo -H pip3 install --upgrade pip
-sudo -H pip3 install networkx numpy regex wrapt biopython
-git clone http://jwgitlab.cs.mcgill.ca/sarrazin/rnabayespairing.git BayesPairing
-cd BayesPairing
-sudo -H pip3 install .
-
-# Train Bayes Pairing (it has been installed on the image and the source has been deleted, we train the models now, and will remount it as volume at run time)
-cd bayespairing/src
-python3 parse_sequences.py -d rna3dmotif -seq ACACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACACCGCCGAGGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAACGAGACGUUAAGCCCACGAGCACUAACAGACCAAAGCCAUCAU -ss ".................................................................((...............)xxxx(...................................................)xxx).............."
-python3 parse_sequences.py -d 3dmotifatlas -seq ACACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACACCGCCGAGGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAACGAGACGUUAAGCCCACGAGCACUAACAGACCAAAGCCAUCAU -ss ".................................................................((...............)xxxx(...................................................)xxx).............."
-cd ../../..
-
-######################################################## Run it ##############################################################
-
-# docker run -v `pwd`/data/modules:/modules -v `pwd`/BayesPairing/bayespairing:/byp -v `pwd`/results:/biorseo/results biorseo ./biorseo.py -i /biorseo/data/fasta/applications.fa --rna3dmotifs --patternmatch --func B
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