Louis BECQUEY / biorseo

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Louis BECQUEY
0b17971f 2 parents ed92d4ff 78f08463

rien^4

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Showing 20 changed files with 12 additions and 47 deletions
...@@ -23,5 +23,11 @@ results/* ...@@ -23,5 +23,11 @@ results/*
23 log_of_the_run.sh 23 log_of_the_run.sh
24 logBadDesc.txt 24 logBadDesc.txt
25 gurobi.log 25 gurobi.log
26 -IL* 26 +temp/*
27 -HL* 27 +
28 +# data
29 +data/modules/BGSU/HL/3.2/diagnostic/*
30 +data/modules/BGSU/HL/3.2/lib/*
31 +data/modules/BGSU/IL/3.2/diagnostic/*
32 +data/modules/BGSU/IL/3.2/lib/*
33 +data/modules/DESC/*.desc
...\ No newline at end of file ...\ No newline at end of file
......
...@@ -2,8 +2,6 @@ ...@@ -2,8 +2,6 @@
2 CPLEXDir="/opt/ibm/ILOG/CPLEX_Studio128" 2 CPLEXDir="/opt/ibm/ILOG/CPLEX_Studio128"
3 IEIGEN="/usr/local/include/eigen3" 3 IEIGEN="/usr/local/include/eigen3"
4 INUPACK="/usr/local/include/nupack" 4 INUPACK="/usr/local/include/nupack"
5 -jar3dexec="/home/persalteas/Software/jar3dbin/jar3d_2014-12-11.jar" 5 +biorseoDir="/nhome/siniac/lbecquey/Software/biorseo"
6 -ILmotifDir="/home/persalteas/Data/RNA/motifs/Matlab_results/IL/3.2/lib" 6 +jar3dexec="/nhome/siniac/lbecquey/Software/jar3dbin/jar3d_2014-12-11.jar"
7 -HLmotifDir="/home/persalteas/Data/RNA/motifs/Matlab_results/HL/3.2/lib" 7 +bypdir="/nhome/siniac/lbecquey/Software/BayesPairing/bayespairing/src"
8 -descfolder="/home/persalteas/Data/RNA/motifs/Rna3Dmotif/No_Redondance_DESC/"
9 -bypdir="/home/persalteas/Software/BayesPairing/bayespairing/src"
......
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1 ->E.coli_alpha_operon_mRNA
2 -UGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGA
3 -(((((((.(((((........[[[[....[[[[....{{{{.))))))))))))..........................]]]].....]]]]...........}}}}
...\ No newline at end of file ...\ No newline at end of file
1 ->E.coli_alpha_operon_mRNA
2 -UGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGA
1 -E.coli_alpha_operon_mRNA
2 -UGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGA
3 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
4 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
5 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
6 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
7 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
8 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
9 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
10 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
11 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
12 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
13 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
14 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
15 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
16 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
17 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
18 -((.((.((..(((((.((...((........))...)).)).))).)).)).))..((..[[))((.((.((..((.((.((.((]].)).)))).)).)).)).)). + 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
19 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
20 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
21 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
22 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
23 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
24 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
25 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
26 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
27 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
28 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
29 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
30 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
31 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
32 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
33 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 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
34 -(((((((.(((((........[[[[....[[[[....{{{{.))))))))))))..........................]]]].....]]]]...........}}}}
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...@@ -8,7 +8,7 @@ ...@@ -8,7 +8,7 @@
8 #include <string> 8 #include <string>
9 #include <vector> 9 #include <vector>
10 10
11 -using Eigen::MatrixXf, Eigen::Matrix; 11 +using Eigen::MatrixXf;
12 using std::map; 12 using std::map;
13 using std::pair; 13 using std::pair;
14 using std::string; 14 using std::string;
......
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