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... | @@ -1003,95 +1003,95 @@ for nt, number in ignored_nt_dict.items(): | ... | @@ -1003,95 +1003,95 @@ for nt, number in ignored_nt_dict.items(): |
1003 | tot = len(RNAcontainer) | 1003 | tot = len(RNAcontainer) |
1004 | print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudoknots." % (tot, pk_counter)) | 1004 | print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudoknots." % (tot, pk_counter)) |
1005 | 1005 | ||
1006 | -# #================= PREDICTION OF STRUCTURES =============================== | 1006 | +#================= PREDICTION OF STRUCTURES =============================== |
1007 | - | 1007 | + |
1008 | -# #define job list | 1008 | +#define job list |
1009 | -# joblist = [] | 1009 | +joblist = [] |
1010 | -# for instance in RNAcontainer: | 1010 | +for instance in RNAcontainer: |
1011 | -# basename = instance.basename | 1011 | + basename = instance.basename |
1012 | -# # RNAsubopt | 1012 | + # RNAsubopt |
1013 | -# joblist.append(Job(command=["RNAsubopt", "-i", outputDir + basename + ".fa", "--outfile="+ basename + ".subopt"], priority=1, checkFunc=check_RNAsubopt, checkArgs=[basename])) | 1013 | + joblist.append(Job(command=["RNAsubopt", "-i", outputDir + basename + ".fa", "--outfile="+ basename + ".subopt"], priority=1, checkFunc=check_RNAsubopt, checkArgs=[basename])) |
1014 | -# joblist.append(Job(command=["mv", basename + ".subopt", outputDir], priority=2, checkFunc=check_RNAsubopt, checkArgs=[basename])) | 1014 | + joblist.append(Job(command=["mv", basename + ".subopt", outputDir], priority=2, checkFunc=check_RNAsubopt, checkArgs=[basename])) |
1015 | -# # JAR3D | 1015 | + # JAR3D |
1016 | -# joblist.append(Job(function=launch_JAR3D, args=[instance.seq_, basename], priority=3, how_many_in_parallel=1, checkFunc=check_JAR3D, checkArgs=[basename])) | 1016 | + joblist.append(Job(function=launch_JAR3D, args=[instance.seq_, basename], priority=3, how_many_in_parallel=1, checkFunc=check_JAR3D, checkArgs=[basename])) |
1017 | -# # BayesPairing and BGSUBayesPairing | 1017 | + # BayesPairing and BGSUBayesPairing |
1018 | -# joblist.append(Job(function=launch_BayesPairing, args=["rna3dmotif", instance.seq_, instance.header_, basename], how_many_in_parallel=-1, priority=3, checkFunc=check_BayesPairing, checkArgs=[basename])) | 1018 | + joblist.append(Job(function=launch_BayesPairing, args=["rna3dmotif", instance.seq_, instance.header_, basename], how_many_in_parallel=-1, priority=3, checkFunc=check_BayesPairing, checkArgs=[basename])) |
1019 | -# joblist.append(Job(function=launch_BayesPairing, args=["3dmotifatlas", instance.seq_, instance.header_, basename], how_many_in_parallel=-1, priority=3, checkFunc=check_BGSUBayesPairing, checkArgs=[basename])) | 1019 | + joblist.append(Job(function=launch_BayesPairing, args=["3dmotifatlas", instance.seq_, instance.header_, basename], how_many_in_parallel=-1, priority=3, checkFunc=check_BGSUBayesPairing, checkArgs=[basename])) |
1020 | -# # biorseoBGSUJAR3DA-D | 1020 | + # biorseoBGSUJAR3DA-D |
1021 | -# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DA, checkArgs=[basename, False])) | 1021 | + joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DA, 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])) | 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 |
1059 | -# jobs = {} | 1059 | +jobs = {} |
1060 | -# jobcount = len(joblist) | 1060 | +jobcount = len(joblist) |
1061 | -# for job in joblist: | 1061 | +for job in joblist: |
1062 | -# if job.priority_ not in jobs.keys(): | 1062 | + if job.priority_ not in jobs.keys(): |
1063 | -# jobs[job.priority_] = {} | 1063 | + jobs[job.priority_] = {} |
1064 | -# if job.nthreads not in jobs[job.priority_].keys(): | 1064 | + if job.nthreads not in jobs[job.priority_].keys(): |
1065 | -# jobs[job.priority_][job.nthreads] = [] | 1065 | + jobs[job.priority_][job.nthreads] = [] |
1066 | -# jobs[job.priority_][job.nthreads].append(job) | 1066 | + jobs[job.priority_][job.nthreads].append(job) |
1067 | -# nprio = max(jobs.keys()) | 1067 | +nprio = max(jobs.keys()) |
1068 | - | 1068 | + |
1069 | - | 1069 | + |
1070 | -# for i in range(1,nprio+1): | 1070 | +for i in range(1,nprio+1): |
1071 | -# if not len(jobs[i].keys()): continue | 1071 | + if not len(jobs[i].keys()): continue |
1072 | - | 1072 | + |
1073 | -# # check the thread numbers | 1073 | + # check the thread numbers |
1074 | -# different_thread_numbers = [n for n in jobs[i].keys()] | 1074 | + different_thread_numbers = [n for n in jobs[i].keys()] |
1075 | -# different_thread_numbers.sort() | 1075 | + different_thread_numbers.sort() |
1076 | - | 1076 | + |
1077 | -# for n in different_thread_numbers: | 1077 | + for n in different_thread_numbers: |
1078 | -# bunch = jobs[i][n] | 1078 | + bunch = jobs[i][n] |
1079 | -# if not len(bunch): continue | 1079 | + if not len(bunch): continue |
1080 | -# pool = MyPool(processes=n) | 1080 | + pool = MyPool(processes=n) |
1081 | -# results = pool.map(execute_job, bunch) | 1081 | + results = pool.map(execute_job, bunch) |
1082 | -# pool.close() | 1082 | + pool.close() |
1083 | -# pool.join() | 1083 | + pool.join() |
1084 | - | 1084 | + |
1085 | -# if len(fails): | 1085 | +if len(fails): |
1086 | -# print() | 1086 | + print() |
1087 | -# print("Some jobs failed! :") | 1087 | + print("Some jobs failed! :") |
1088 | -# print() | 1088 | + print() |
1089 | -# for j in fails: | 1089 | + for j in fails: |
1090 | -# print(j.cmd_) | 1090 | + print(j.cmd_) |
1091 | -# else: | 1091 | +else: |
1092 | -# print() | 1092 | + print() |
1093 | -# print("Computations ran successfully.") | 1093 | + print("Computations ran successfully.") |
1094 | -# print() | 1094 | + print() |
1095 | 1095 | ||
1096 | 1096 | ||
1097 | # ================= Statistics (without pseudoknots) ======================== | 1097 | # ================= Statistics (without pseudoknots) ======================== | ... | ... |
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