Louis BECQUEY / biorseo

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Louis BECQUEY
7675e524 1 parent 9bd1c85e

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# Please set the following variables to the correct paths :
CPLEXDir="/opt/ibm/ILOG/CPLEX_Studio128_Student"
CPLEXDir="/opt/ibm/ILOG/CPLEX_Studio128"
IEIGEN="/usr/local/include/eigen3"
INUPACK="/usr/local/include/nupack"
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
jar3dexec="/home/persalteas/Software/jar3dbin/jar3d_2014-12-11.jar"
ILmotifDir="/home/persalteas/Data/RNA/motifs/Matlab_results/IL/3.2/lib"
HLmotifDir="/home/persalteas/Data/RNA/motifs/Matlab_results/HL/3.2/lib"
descfolder="/home/persalteas/Data/RNA/motifs/No_Redondance_DESC/"
bypdir="/home/persalteas/Software/BayesPairing/bayespairing/src"
biorseoDir="/home/persalteas/Software/biorseo"
......
......@@ -1022,37 +1022,37 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# # biorseoBGSUBayesPairA-D
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# # biorseoBayesPairA-D
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# # biorseoRawA,B
# 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]))
# 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]))
# 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]))
# 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]))
# # RNA MoIP
# joblist.append(Job(function=launch_RNAMoIP, args=[instance.seq_, instance.header_, basename], priority=3, timeout=3600, checkFunc=check_RNAMoIP, checkArgs=[basename]))
# # Biokop
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# # biorseoBGSUBayesPairA-D
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# biorseoBayesPairA-D
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# 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]))
# biorseoRawA,B
# 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]))
# 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]))
# 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]))
# 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]))
# RNA MoIP
# joblist.append(Job(function=launch_RNAMoIP, args=[instance.seq_, instance.header_, basename], priority=3, timeout=3600, checkFunc=check_RNAMoIP, checkArgs=[basename]))
# Biokop
# 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]))
# # execute jobs
......@@ -1291,104 +1291,104 @@ print("Wilcoxon signed rank test with PK: H0 = 'The position parameter of Biokop
# r.biorseoBGSUBayesPairD ], labels):
# print(name+":\t",m.best_pred)
# # ================= PLOTS OF RESULTS =======================================
# merge = [ x_PK_fully[0], # Biokop
# x_noPK_fully[0], # RNA subopt
# x_noPK_fully[1], # RNA MoIP
# x_noPK_fully[2], x_PK_fully[2], #biorseoRawA
# x_noPK_fully[3], x_PK_fully[3], #biorseoRawB
# x_noPK_fully[4], x_PK_fully[4], #biorseoBayesPairA
# x_noPK_fully[5], x_PK_fully[5], #biorseoBayesPairB
# x_noPK_fully[6], x_PK_fully[6], #biorseoBayesPairC
# x_noPK_fully[7], x_PK_fully[7], #biorseoBayesPairD
# x_noPK_fully[8], x_PK_fully[8], #biorseoBGSUJAR3DA
# x_noPK_fully[9], x_PK_fully[9], #biorseoBGSUJAR3DB
# x_noPK_fully[10], x_PK_fully[10], #biorseoBGSUJAR3DC
# x_noPK_fully[11], x_PK_fully[11], #biorseoBGSUJAR3DD
# x_noPK_fully[12], x_PK_fully[12], #biorseoBGSUBayesPairA
# x_noPK_fully[13], x_PK_fully[13], #biorseoBGSUBayesPairB
# x_noPK_fully[14], x_PK_fully[14], #biorseoBGSUBayesPairC
# x_noPK_fully[15], x_PK_fully[15], #biorseoBGSUBayesPairD
# ]
# ================= PLOTS OF RESULTS =======================================
merge = [ x_PK_fully[0], # Biokop
x_noPK_fully[0], # RNA subopt
x_noPK_fully[1], # RNA MoIP
x_noPK_fully[2], x_PK_fully[2], #biorseoRawA
x_noPK_fully[3], x_PK_fully[3], #biorseoRawB
x_noPK_fully[4], x_PK_fully[4], #biorseoBayesPairA
x_noPK_fully[5], x_PK_fully[5], #biorseoBayesPairB
x_noPK_fully[6], x_PK_fully[6], #biorseoBayesPairC
x_noPK_fully[7], x_PK_fully[7], #biorseoBayesPairD
x_noPK_fully[8], x_PK_fully[8], #biorseoBGSUJAR3DA
x_noPK_fully[9], x_PK_fully[9], #biorseoBGSUJAR3DB
x_noPK_fully[10], x_PK_fully[10], #biorseoBGSUJAR3DC
x_noPK_fully[11], x_PK_fully[11], #biorseoBGSUJAR3DD
x_noPK_fully[12], x_PK_fully[12], #biorseoBGSUBayesPairA
x_noPK_fully[13], x_PK_fully[13], #biorseoBGSUBayesPairB
x_noPK_fully[14], x_PK_fully[14], #biorseoBGSUBayesPairC
x_noPK_fully[15], x_PK_fully[15], #biorseoBGSUBayesPairD
]
# colors = [ 'green', 'blue', 'goldenrod',
# 'darkturquoise', 'darkturquoise',
# 'red', 'red',
# 'firebrick', 'firebrick',
# 'limegreen', 'limegreen',
# 'olive', 'olive',
# 'forestgreen', 'forestgreen',
# 'lime', 'lime',
# 'darkcyan', 'darkcyan',
# 'royalblue', 'royalblue',
# 'navy', 'navy',
# 'limegreen', 'limegreen',
# 'olive', 'olive',
# 'forestgreen', 'forestgreen',
# 'lime', 'lime'
# ]
# labels = [ "Biokop", "RNAsubopt",
# "RNA MoIP",
# "$f_{1A}$",
# "$f_{1B}$",
# "$f_{1A}$",
# "$f_{1B}$",
# "$f_{1C}$",
# "$f_{1D}$",
# "$f_{1A}$",
# "$f_{1B}$",
# "$f_{1C}$",
# "$f_{1D}$",
# "$f_{1A}$",
# "$f_{1B}$",
# "$f_{1C}$",
# "$f_{1D}$"
# ]
colors = [ 'green', 'blue', 'goldenrod',
'darkturquoise', 'darkturquoise',
'red', 'red',
'firebrick', 'firebrick',
'limegreen', 'limegreen',
'olive', 'olive',
'forestgreen', 'forestgreen',
'lime', 'lime',
'darkcyan', 'darkcyan',
'royalblue', 'royalblue',
'navy', 'navy',
'limegreen', 'limegreen',
'olive', 'olive',
'forestgreen', 'forestgreen',
'lime', 'lime'
]
labels = [ "Biokop", "RNAsubopt",
"RNA MoIP",
"$f_{1A}$",
"$f_{1B}$",
"$f_{1A}$",
"$f_{1B}$",
"$f_{1C}$",
"$f_{1D}$",
"$f_{1A}$",
"$f_{1B}$",
"$f_{1C}$",
"$f_{1D}$",
"$f_{1A}$",
"$f_{1B}$",
"$f_{1C}$",
"$f_{1D}$"
]
# ax = plt.subplot(211)
# ax.tick_params(labelsize=12)
# for y in [ i/10 for i in range(11) ]:
# plt.axhline(y=y, color="grey", linestyle="--", linewidth=1)
# colors = [ 'blue','goldenrod',
# 'red', 'firebrick','limegreen','olive', 'forestgreen', 'lime',
# 'darkturquoise', 'darkcyan', 'royalblue', 'navy', 'limegreen','olive', 'forestgreen', 'lime'
# ]
# bplot = plt.boxplot(x_noPK_fully, vert=True, patch_artist=True, notch=False, whis=[3,97])
# for patch, color in zip(bplot['boxes'], colors):
# patch.set_facecolor(color)
# # plt.axhline(y=0, color="black", linewidth=1)
# # plt.axhline(y=1, color="black", linewidth=1)
# plt.xticks([1.0+i for i in range(16)], labels[1:])
# plt.ylim((0.5, 1.01))
# plt.ylabel("MCC", fontsize=12)
# plt.subplots_adjust(left=0.05, right=0.95)
# plt.title("Performance without pseudoknots (%d RNAs included)" % len(x_noPK_fully[0]))
# ax = plt.subplot(212)
# ax.tick_params(top=True, bottom=False, labeltop=True, labelbottom=False, labelsize=12)
# ax.xaxis.set_label_position('top')
# for y in [ i/10 for i in range(11) ]:
# plt.axhline(y=y, color="grey", linestyle="--", linewidth=1)
# colors = [ 'green','green',
# 'red', 'firebrick','limegreen','olive', 'forestgreen', 'lime',
# 'darkturquoise', 'darkcyan', 'royalblue', 'navy', 'limegreen','olive', 'forestgreen', 'lime'
# ]
# labels = [ "Biokop"]
# bplot = plt.boxplot(x_PK_fully, vert=True, patch_artist=True, notch=False, whis=[3,97])
# for patch, color in zip(bplot['boxes'], colors):
# patch.set_facecolor(color)
# # plt.axhline(y=0, color="black", linewidth=1)
# # plt.axhline(y=1, color="black", linewidth=1)
# plt.xticks([1.0+i for i in range(16)], labels)
# plt.ylim((0.5, 1.01))
# plt.ylabel("MCC", fontsize=12)
# plt.subplots_adjust(left=0.05, right=0.95)
# plt.text(6.2,-0.3,"Performance with pseudoknots (%d RNAs included)" % len(x_PK_fully[0]), fontsize=12)
ax = plt.subplot(211)
ax.tick_params(labelsize=12)
for y in [ i/10 for i in range(11) ]:
plt.axhline(y=y, color="grey", linestyle="--", linewidth=1)
colors = [ 'blue','goldenrod',
'red', 'firebrick','limegreen','olive', 'forestgreen', 'lime',
'darkturquoise', 'darkcyan', 'royalblue', 'navy', 'limegreen','olive', 'forestgreen', 'lime'
]
bplot = plt.boxplot(x_noPK_fully, vert=True, patch_artist=True, notch=False, whis=[3,97])
for patch, color in zip(bplot['boxes'], colors):
patch.set_facecolor(color)
# plt.axhline(y=0, color="black", linewidth=1)
# plt.axhline(y=1, color="black", linewidth=1)
plt.xticks([1.0+i for i in range(16)], labels[1:])
plt.ylim((0.5, 1.01))
plt.ylabel("MCC", fontsize=12)
plt.subplots_adjust(left=0.05, right=0.95)
plt.title("Performance without pseudoknots (%d RNAs included)" % len(x_noPK_fully[0]))
ax = plt.subplot(212)
ax.tick_params(top=True, bottom=False, labeltop=True, labelbottom=False, labelsize=12)
ax.xaxis.set_label_position('top')
for y in [ i/10 for i in range(11) ]:
plt.axhline(y=y, color="grey", linestyle="--", linewidth=1)
colors = [ 'green','green',
'red', 'firebrick','limegreen','olive', 'forestgreen', 'lime',
'darkturquoise', 'darkcyan', 'royalblue', 'navy', 'limegreen','olive', 'forestgreen', 'lime'
]
labels = [ "Biokop"]
bplot = plt.boxplot(x_PK_fully, vert=True, patch_artist=True, notch=False, whis=[3,97])
for patch, color in zip(bplot['boxes'], colors):
patch.set_facecolor(color)
# plt.axhline(y=0, color="black", linewidth=1)
# plt.axhline(y=1, color="black", linewidth=1)
plt.xticks([1.0+i for i in range(16)], labels)
plt.ylim((0.5, 1.01))
plt.ylabel("MCC", fontsize=12)
plt.subplots_adjust(left=0.05, right=0.95)
plt.text(6.2,-0.3,"Performance with pseudoknots (%d RNAs included)" % len(x_PK_fully[0]), fontsize=12)
# plt.show()
plt.show()
# ================== MCC performance ====================================
......