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Louis BECQUEY
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biorseo
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Authored by
Louis BECQUEY
2019-06-04 17:13:18 +0200
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7675e5244339d0dcf5ef5040bdaf6e8858f09e77
7675e524
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9bd1c85e
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test_on_RNAstrand.py
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View file @
7675e52
# 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"
...
...
test_on_RNAstrand.py
View file @
7675e52
...
...
@@ -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 ====================================
...
...
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