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18 changed files
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10 additions
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46 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 | ... | ... |
... | @@ -2,9 +2,6 @@ | ... | @@ -2,9 +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 | +biorseoDir="/home/persalteas/Software/biorseo" | ||
5 | jar3dexec="/home/persalteas/Software/jar3dbin/jar3d_2014-12-11.jar" | 6 | jar3dexec="/home/persalteas/Software/jar3dbin/jar3d_2014-12-11.jar" |
6 | -ILmotifDir="/home/persalteas/Data/RNA/motifs/Matlab_results/IL/3.2/lib" | ||
7 | -HLmotifDir="/home/persalteas/Data/RNA/motifs/Matlab_results/HL/3.2/lib" | ||
8 | -descfolder="/home/persalteas/Data/RNA/motifs/No_Redondance_DESC/" | ||
9 | bypdir="/home/persalteas/Software/BayesPairing/bayespairing/src" | 7 | bypdir="/home/persalteas/Software/BayesPairing/bayespairing/src" |
10 | -biorseoDir="/home/persalteas/Software/biorseo" | ... | ... |
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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 | ||
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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biorseo.py
0 → 100644
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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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