Louis BECQUEY / biorseo

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Louis BECQUEY
7675e524 1 parent 9bd1c85e

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1 # Please set the following variables to the correct paths : 1 # Please set the following variables to the correct paths :
2 -CPLEXDir="/opt/ibm/ILOG/CPLEX_Studio128_Student" 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="/nhome/siniac/lbecquey/Software/jar3dbin/jar3d_2014-12-11.jar"
6 -ILmotifDir="/nhome/siniac/lbecquey/Data/RNA/motifs/BGSU/Matlab_results/IL/3.2/lib"
7 -HLmotifDir="/nhome/siniac/lbecquey/Data/RNA/motifs/BGSU/Matlab_results/HL/3.2/lib"
8 -descfolder="/local/local/labo/03_tests_biominserter/No_Redondance_DESC/"
9 -bypdir="/nhome/siniac/lbecquey/Software/BayesPairing/bayespairing/src"
10 -biorseoDir="/nhome/siniac/lbecquey/Software/biorseo"
...\ No newline at end of file ...\ No newline at end of file
5 +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"
10 +biorseoDir="/home/persalteas/Software/biorseo"
......
...@@ -1022,37 +1022,37 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno ...@@ -1022,37 +1022,37 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno
1022 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DB, checkArgs=[basename, False])) 1022 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DB, checkArgs=[basename, False]))
1023 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DC, checkArgs=[basename, False])) 1023 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DC, checkArgs=[basename, False]))
1024 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dD", "--type", "D", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DD, checkArgs=[basename, False])) 1024 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dD", "--type", "D", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DD, checkArgs=[basename, False]))
1025 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dA", "--type", "A"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DA, checkArgs=[basename, True])) 1025 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dA", "--type", "A"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DA, checkArgs=[basename, True]))
1026 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DB, checkArgs=[basename, True])) 1026 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DB, checkArgs=[basename, True]))
1027 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dC", "--type", "C"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DC, checkArgs=[basename, True])) 1027 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dC", "--type", "C"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DC, checkArgs=[basename, True]))
1028 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dD", "--type", "D"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DD, checkArgs=[basename, True])) 1028 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dD", "--type", "D"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DD, checkArgs=[basename, True]))
1029 -# # biorseoBGSUBayesPairA-D 1029 + # # biorseoBGSUBayesPairA-D
1030 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairA, checkArgs=[basename, False])) 1030 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairA, checkArgs=[basename, False]))
1031 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairB, checkArgs=[basename, False])) 1031 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairB, checkArgs=[basename, False]))
1032 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairC, checkArgs=[basename, False])) 1032 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairC, checkArgs=[basename, False]))
1033 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypD", "--type", "D", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairD, checkArgs=[basename, False])) 1033 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypD", "--type", "D", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairD, checkArgs=[basename, False]))
1034 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypA", "--type", "A"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairA, checkArgs=[basename, True])) 1034 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypA", "--type", "A"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairA, checkArgs=[basename, True]))
1035 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairB, checkArgs=[basename, True])) 1035 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairB, checkArgs=[basename, True]))
1036 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypC", "--type", "C"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairC, checkArgs=[basename, True])) 1036 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypC", "--type", "C"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairC, checkArgs=[basename, True]))
1037 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypD", "--type", "D"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairD, checkArgs=[basename, True])) 1037 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypD", "--type", "D"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairD, checkArgs=[basename, True]))
1038 -# # biorseoBayesPairA-D 1038 + # biorseoBayesPairA-D
1039 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairA, checkArgs=[basename, False])) 1039 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairA, checkArgs=[basename, False]))
1040 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairB, checkArgs=[basename, False])) 1040 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairB, checkArgs=[basename, False]))
1041 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairC, checkArgs=[basename, False])) 1041 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairC, checkArgs=[basename, False]))
1042 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypD", "--type", "D", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairD, checkArgs=[basename, False])) 1042 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypD", "--type", "D", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairD, checkArgs=[basename, False]))
1043 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"PK/"+basename+".bypA", "--type", "A"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairA, checkArgs=[basename, True])) 1043 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"PK/"+basename+".bypA", "--type", "A"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairA, checkArgs=[basename, True]))
1044 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"PK/"+basename+".bypB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairB, checkArgs=[basename, True])) 1044 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"PK/"+basename+".bypB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairB, checkArgs=[basename, True]))
1045 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"PK/"+basename+".bypC", "--type", "C"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairC, checkArgs=[basename, True])) 1045 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"PK/"+basename+".bypC", "--type", "C"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairC, checkArgs=[basename, True]))
1046 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"PK/"+basename+".bypD", "--type", "D"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairD, checkArgs=[basename, True])) 1046 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"PK/"+basename+".bypD", "--type", "D"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairD, checkArgs=[basename, True]))
1047 -# # biorseoRawA,B 1047 + # biorseoRawA,B
1048 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir + basename + ".fa", "-d", descfolder, "-o", outputDir+"noPK/" + basename + ".rawA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoRawA, checkArgs=[basename, False])) 1048 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir + basename + ".fa", "-d", descfolder, "-o", outputDir+"noPK/" + basename + ".rawA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoRawA, checkArgs=[basename, False]))
1049 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir + basename + ".fa", "-d", descfolder, "-o", outputDir+"noPK/" + basename + ".rawB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoRawB, checkArgs=[basename, False])) 1049 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir + basename + ".fa", "-d", descfolder, "-o", outputDir+"noPK/" + basename + ".rawB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoRawB, checkArgs=[basename, False]))
1050 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir + basename + ".fa", "-d", descfolder, "-o", outputDir+"PK/" + basename + ".rawA", "--type", "A"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoRawA, checkArgs=[basename, True])) 1050 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir + basename + ".fa", "-d", descfolder, "-o", outputDir+"PK/" + basename + ".rawA", "--type", "A"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoRawA, checkArgs=[basename, True]))
1051 -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir + basename + ".fa", "-d", descfolder, "-o", outputDir+"PK/" + basename + ".rawB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoRawB, checkArgs=[basename, True])) 1051 + # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir + basename + ".fa", "-d", descfolder, "-o", outputDir+"PK/" + basename + ".rawB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoRawB, checkArgs=[basename, True]))
1052 -# # RNA MoIP 1052 + # RNA MoIP
1053 -# joblist.append(Job(function=launch_RNAMoIP, args=[instance.seq_, instance.header_, basename], priority=3, timeout=3600, checkFunc=check_RNAMoIP, checkArgs=[basename])) 1053 + # joblist.append(Job(function=launch_RNAMoIP, args=[instance.seq_, instance.header_, basename], priority=3, timeout=3600, checkFunc=check_RNAMoIP, checkArgs=[basename]))
1054 -# # Biokop 1054 + # Biokop
1055 -# joblist.append(Job(command=[biorseoDir + "/../biokop/biokop", "-n1", "-i", outputDir + basename + ".fa", "-o", outputDir + basename + ".biok"], priority=5, timeout=15000, how_many_in_parallel=3, checkFunc=check_biokop, checkArgs=[basename])) 1055 + # joblist.append(Job(command=[biorseoDir + "/../biokop/biokop", "-n1", "-i", outputDir + basename + ".fa", "-o", outputDir + basename + ".biok"], priority=5, timeout=15000, how_many_in_parallel=3, checkFunc=check_biokop, checkArgs=[basename]))
1056 1056
1057 1057
1058 # # execute jobs 1058 # # execute jobs
...@@ -1291,104 +1291,104 @@ print("Wilcoxon signed rank test with PK: H0 = 'The position parameter of Biokop ...@@ -1291,104 +1291,104 @@ print("Wilcoxon signed rank test with PK: H0 = 'The position parameter of Biokop
1291 # r.biorseoBGSUBayesPairD ], labels): 1291 # r.biorseoBGSUBayesPairD ], labels):
1292 # print(name+":\t",m.best_pred) 1292 # print(name+":\t",m.best_pred)
1293 1293
1294 -# # ================= PLOTS OF RESULTS ======================================= 1294 +# ================= PLOTS OF RESULTS =======================================
1295 - 1295 +
1296 -# merge = [ x_PK_fully[0], # Biokop 1296 +merge = [ x_PK_fully[0], # Biokop
1297 -# x_noPK_fully[0], # RNA subopt 1297 + x_noPK_fully[0], # RNA subopt
1298 -# x_noPK_fully[1], # RNA MoIP 1298 + x_noPK_fully[1], # RNA MoIP
1299 -# x_noPK_fully[2], x_PK_fully[2], #biorseoRawA 1299 + x_noPK_fully[2], x_PK_fully[2], #biorseoRawA
1300 -# x_noPK_fully[3], x_PK_fully[3], #biorseoRawB 1300 + x_noPK_fully[3], x_PK_fully[3], #biorseoRawB
1301 -# x_noPK_fully[4], x_PK_fully[4], #biorseoBayesPairA 1301 + x_noPK_fully[4], x_PK_fully[4], #biorseoBayesPairA
1302 -# x_noPK_fully[5], x_PK_fully[5], #biorseoBayesPairB 1302 + x_noPK_fully[5], x_PK_fully[5], #biorseoBayesPairB
1303 -# x_noPK_fully[6], x_PK_fully[6], #biorseoBayesPairC 1303 + x_noPK_fully[6], x_PK_fully[6], #biorseoBayesPairC
1304 -# x_noPK_fully[7], x_PK_fully[7], #biorseoBayesPairD 1304 + x_noPK_fully[7], x_PK_fully[7], #biorseoBayesPairD
1305 -# x_noPK_fully[8], x_PK_fully[8], #biorseoBGSUJAR3DA 1305 + x_noPK_fully[8], x_PK_fully[8], #biorseoBGSUJAR3DA
1306 -# x_noPK_fully[9], x_PK_fully[9], #biorseoBGSUJAR3DB 1306 + x_noPK_fully[9], x_PK_fully[9], #biorseoBGSUJAR3DB
1307 -# x_noPK_fully[10], x_PK_fully[10], #biorseoBGSUJAR3DC 1307 + x_noPK_fully[10], x_PK_fully[10], #biorseoBGSUJAR3DC
1308 -# x_noPK_fully[11], x_PK_fully[11], #biorseoBGSUJAR3DD 1308 + x_noPK_fully[11], x_PK_fully[11], #biorseoBGSUJAR3DD
1309 -# x_noPK_fully[12], x_PK_fully[12], #biorseoBGSUBayesPairA 1309 + x_noPK_fully[12], x_PK_fully[12], #biorseoBGSUBayesPairA
1310 -# x_noPK_fully[13], x_PK_fully[13], #biorseoBGSUBayesPairB 1310 + x_noPK_fully[13], x_PK_fully[13], #biorseoBGSUBayesPairB
1311 -# x_noPK_fully[14], x_PK_fully[14], #biorseoBGSUBayesPairC 1311 + x_noPK_fully[14], x_PK_fully[14], #biorseoBGSUBayesPairC
1312 -# x_noPK_fully[15], x_PK_fully[15], #biorseoBGSUBayesPairD 1312 + x_noPK_fully[15], x_PK_fully[15], #biorseoBGSUBayesPairD
1313 -# ] 1313 +]
1314 1314
1315 -# colors = [ 'green', 'blue', 'goldenrod', 1315 +colors = [ 'green', 'blue', 'goldenrod',
1316 -# 'darkturquoise', 'darkturquoise', 1316 + 'darkturquoise', 'darkturquoise',
1317 -# 'red', 'red', 1317 + 'red', 'red',
1318 -# 'firebrick', 'firebrick', 1318 + 'firebrick', 'firebrick',
1319 -# 'limegreen', 'limegreen', 1319 + 'limegreen', 'limegreen',
1320 -# 'olive', 'olive', 1320 + 'olive', 'olive',
1321 -# 'forestgreen', 'forestgreen', 1321 + 'forestgreen', 'forestgreen',
1322 -# 'lime', 'lime', 1322 + 'lime', 'lime',
1323 -# 'darkcyan', 'darkcyan', 1323 + 'darkcyan', 'darkcyan',
1324 -# 'royalblue', 'royalblue', 1324 + 'royalblue', 'royalblue',
1325 -# 'navy', 'navy', 1325 + 'navy', 'navy',
1326 -# 'limegreen', 'limegreen', 1326 + 'limegreen', 'limegreen',
1327 -# 'olive', 'olive', 1327 + 'olive', 'olive',
1328 -# 'forestgreen', 'forestgreen', 1328 + 'forestgreen', 'forestgreen',
1329 -# 'lime', 'lime' 1329 + 'lime', 'lime'
1330 -# ] 1330 +]
1331 -# labels = [ "Biokop", "RNAsubopt", 1331 +labels = [ "Biokop", "RNAsubopt",
1332 -# "RNA MoIP", 1332 + "RNA MoIP",
1333 -# "$f_{1A}$", 1333 + "$f_{1A}$",
1334 -# "$f_{1B}$", 1334 + "$f_{1B}$",
1335 -# "$f_{1A}$", 1335 + "$f_{1A}$",
1336 -# "$f_{1B}$", 1336 + "$f_{1B}$",
1337 -# "$f_{1C}$", 1337 + "$f_{1C}$",
1338 -# "$f_{1D}$", 1338 + "$f_{1D}$",
1339 -# "$f_{1A}$", 1339 + "$f_{1A}$",
1340 -# "$f_{1B}$", 1340 + "$f_{1B}$",
1341 -# "$f_{1C}$", 1341 + "$f_{1C}$",
1342 -# "$f_{1D}$", 1342 + "$f_{1D}$",
1343 -# "$f_{1A}$", 1343 + "$f_{1A}$",
1344 -# "$f_{1B}$", 1344 + "$f_{1B}$",
1345 -# "$f_{1C}$", 1345 + "$f_{1C}$",
1346 -# "$f_{1D}$" 1346 + "$f_{1D}$"
1347 -# ] 1347 +]
1348 1348
1349 -# ax = plt.subplot(211) 1349 +ax = plt.subplot(211)
1350 -# ax.tick_params(labelsize=12) 1350 +ax.tick_params(labelsize=12)
1351 -# for y in [ i/10 for i in range(11) ]: 1351 +for y in [ i/10 for i in range(11) ]:
1352 -# plt.axhline(y=y, color="grey", linestyle="--", linewidth=1) 1352 + plt.axhline(y=y, color="grey", linestyle="--", linewidth=1)
1353 -# colors = [ 'blue','goldenrod', 1353 +colors = [ 'blue','goldenrod',
1354 -# 'red', 'firebrick','limegreen','olive', 'forestgreen', 'lime', 1354 + 'red', 'firebrick','limegreen','olive', 'forestgreen', 'lime',
1355 -# 'darkturquoise', 'darkcyan', 'royalblue', 'navy', 'limegreen','olive', 'forestgreen', 'lime' 1355 + 'darkturquoise', 'darkcyan', 'royalblue', 'navy', 'limegreen','olive', 'forestgreen', 'lime'
1356 -# ] 1356 + ]
1357 -# bplot = plt.boxplot(x_noPK_fully, vert=True, patch_artist=True, notch=False, whis=[3,97]) 1357 +bplot = plt.boxplot(x_noPK_fully, vert=True, patch_artist=True, notch=False, whis=[3,97])
1358 -# for patch, color in zip(bplot['boxes'], colors): 1358 +for patch, color in zip(bplot['boxes'], colors):
1359 -# patch.set_facecolor(color) 1359 + patch.set_facecolor(color)
1360 -# # plt.axhline(y=0, color="black", linewidth=1) 1360 +# plt.axhline(y=0, color="black", linewidth=1)
1361 -# # plt.axhline(y=1, color="black", linewidth=1) 1361 +# plt.axhline(y=1, color="black", linewidth=1)
1362 -# plt.xticks([1.0+i for i in range(16)], labels[1:]) 1362 +plt.xticks([1.0+i for i in range(16)], labels[1:])
1363 -# plt.ylim((0.5, 1.01)) 1363 +plt.ylim((0.5, 1.01))
1364 -# plt.ylabel("MCC", fontsize=12) 1364 +plt.ylabel("MCC", fontsize=12)
1365 -# plt.subplots_adjust(left=0.05, right=0.95) 1365 +plt.subplots_adjust(left=0.05, right=0.95)
1366 -# plt.title("Performance without pseudoknots (%d RNAs included)" % len(x_noPK_fully[0])) 1366 +plt.title("Performance without pseudoknots (%d RNAs included)" % len(x_noPK_fully[0]))
1367 - 1367 +
1368 - 1368 +
1369 -# ax = plt.subplot(212) 1369 +ax = plt.subplot(212)
1370 -# ax.tick_params(top=True, bottom=False, labeltop=True, labelbottom=False, labelsize=12) 1370 +ax.tick_params(top=True, bottom=False, labeltop=True, labelbottom=False, labelsize=12)
1371 -# ax.xaxis.set_label_position('top') 1371 +ax.xaxis.set_label_position('top')
1372 -# for y in [ i/10 for i in range(11) ]: 1372 +for y in [ i/10 for i in range(11) ]:
1373 -# plt.axhline(y=y, color="grey", linestyle="--", linewidth=1) 1373 + plt.axhline(y=y, color="grey", linestyle="--", linewidth=1)
1374 -# colors = [ 'green','green', 1374 +colors = [ 'green','green',
1375 -# 'red', 'firebrick','limegreen','olive', 'forestgreen', 'lime', 1375 + 'red', 'firebrick','limegreen','olive', 'forestgreen', 'lime',
1376 -# 'darkturquoise', 'darkcyan', 'royalblue', 'navy', 'limegreen','olive', 'forestgreen', 'lime' 1376 + 'darkturquoise', 'darkcyan', 'royalblue', 'navy', 'limegreen','olive', 'forestgreen', 'lime'
1377 -# ] 1377 + ]
1378 -# labels = [ "Biokop"] 1378 +labels = [ "Biokop"]
1379 -# bplot = plt.boxplot(x_PK_fully, vert=True, patch_artist=True, notch=False, whis=[3,97]) 1379 +bplot = plt.boxplot(x_PK_fully, vert=True, patch_artist=True, notch=False, whis=[3,97])
1380 -# for patch, color in zip(bplot['boxes'], colors): 1380 +for patch, color in zip(bplot['boxes'], colors):
1381 -# patch.set_facecolor(color) 1381 + patch.set_facecolor(color)
1382 -# # plt.axhline(y=0, color="black", linewidth=1) 1382 +# plt.axhline(y=0, color="black", linewidth=1)
1383 -# # plt.axhline(y=1, color="black", linewidth=1) 1383 +# plt.axhline(y=1, color="black", linewidth=1)
1384 -# plt.xticks([1.0+i for i in range(16)], labels) 1384 +plt.xticks([1.0+i for i in range(16)], labels)
1385 -# plt.ylim((0.5, 1.01)) 1385 +plt.ylim((0.5, 1.01))
1386 -# plt.ylabel("MCC", fontsize=12) 1386 +plt.ylabel("MCC", fontsize=12)
1387 -# plt.subplots_adjust(left=0.05, right=0.95) 1387 +plt.subplots_adjust(left=0.05, right=0.95)
1388 -# plt.text(6.2,-0.3,"Performance with pseudoknots (%d RNAs included)" % len(x_PK_fully[0]), fontsize=12) 1388 +plt.text(6.2,-0.3,"Performance with pseudoknots (%d RNAs included)" % len(x_PK_fully[0]), fontsize=12)
1389 1389
1390 1390
1391 -# plt.show() 1391 +plt.show()
1392 1392
1393 1393
1394 # ================== MCC performance ==================================== 1394 # ================== MCC performance ====================================
......