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/
biorseo
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Authored by
Louis BECQUEY
2019-06-04 19:38:22 +0200
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4b6bc7b377c7aac7c2f0e1b442cd9a3c62bb9e83
4b6bc7b3
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test_on_RNAstrand.py
test_on_RNAstrand.py
View file @
4b6bc7b
...
...
@@ -1003,95 +1003,95 @@ for nt, number in ignored_nt_dict.items():
tot
=
len
(
RNAcontainer
)
print
(
"Loaded
%
d RNAs of length between 10 and 100.
%
d of them contain pseudoknots."
%
(
tot
,
pk_counter
))
#
#
================= PREDICTION OF STRUCTURES ===============================
#
#
define job list
#
joblist = []
#
for instance in RNAcontainer:
#
basename = instance.basename
#
# RNAsubopt
#
joblist.append(Job(command=["RNAsubopt", "-i", outputDir + basename + ".fa", "--outfile="+ basename + ".subopt"], priority=1, checkFunc=check_RNAsubopt, checkArgs=[basename]))
#
joblist.append(Job(command=["mv", basename + ".subopt", outputDir], priority=2, checkFunc=check_RNAsubopt, checkArgs=[basename]))
#
# JAR3D
#
joblist.append(Job(function=launch_JAR3D, args=[instance.seq_, basename], priority=3, how_many_in_parallel=1, checkFunc=check_JAR3D, checkArgs=[basename]))
#
# BayesPairing and BGSUBayesPairing
#
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]))
#
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]))
#
# biorseoBGSUJAR3DA-D
#
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]))
#
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]))
#
#
execute jobs
#
jobs = {}
#
jobcount = len(joblist)
#
for job in joblist:
#
if job.priority_ not in jobs.keys():
#
jobs[job.priority_] = {}
#
if job.nthreads not in jobs[job.priority_].keys():
#
jobs[job.priority_][job.nthreads] = []
#
jobs[job.priority_][job.nthreads].append(job)
#
nprio = max(jobs.keys())
#
for i in range(1,nprio+1):
#
if not len(jobs[i].keys()): continue
#
# check the thread numbers
#
different_thread_numbers = [n for n in jobs[i].keys()]
#
different_thread_numbers.sort()
#
for n in different_thread_numbers:
#
bunch = jobs[i][n]
#
if not len(bunch): continue
#
pool = MyPool(processes=n)
#
results = pool.map(execute_job, bunch)
#
pool.close()
#
pool.join()
#
if len(fails):
#
print()
#
print("Some jobs failed! :")
#
print()
#
for j in fails:
#
print(j.cmd_)
#
else:
#
print()
#
print("Computations ran successfully.")
#
print()
#================= PREDICTION OF STRUCTURES ===============================
#define job list
joblist
=
[]
for
instance
in
RNAcontainer
:
basename
=
instance
.
basename
# RNAsubopt
joblist
.
append
(
Job
(
command
=
[
"RNAsubopt"
,
"-i"
,
outputDir
+
basename
+
".fa"
,
"--outfile="
+
basename
+
".subopt"
],
priority
=
1
,
checkFunc
=
check_RNAsubopt
,
checkArgs
=
[
basename
]))
joblist
.
append
(
Job
(
command
=
[
"mv"
,
basename
+
".subopt"
,
outputDir
],
priority
=
2
,
checkFunc
=
check_RNAsubopt
,
checkArgs
=
[
basename
]))
# JAR3D
joblist
.
append
(
Job
(
function
=
launch_JAR3D
,
args
=
[
instance
.
seq_
,
basename
],
priority
=
3
,
how_many_in_parallel
=
1
,
checkFunc
=
check_JAR3D
,
checkArgs
=
[
basename
]))
# BayesPairing and BGSUBayesPairing
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
]))
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
]))
# biorseoBGSUJAR3DA-D
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
]))
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
]))
# execute jobs
jobs
=
{}
jobcount
=
len
(
joblist
)
for
job
in
joblist
:
if
job
.
priority_
not
in
jobs
.
keys
():
jobs
[
job
.
priority_
]
=
{}
if
job
.
nthreads
not
in
jobs
[
job
.
priority_
]
.
keys
():
jobs
[
job
.
priority_
][
job
.
nthreads
]
=
[]
jobs
[
job
.
priority_
][
job
.
nthreads
]
.
append
(
job
)
nprio
=
max
(
jobs
.
keys
())
for
i
in
range
(
1
,
nprio
+
1
):
if
not
len
(
jobs
[
i
]
.
keys
()):
continue
# check the thread numbers
different_thread_numbers
=
[
n
for
n
in
jobs
[
i
]
.
keys
()]
different_thread_numbers
.
sort
()
for
n
in
different_thread_numbers
:
bunch
=
jobs
[
i
][
n
]
if
not
len
(
bunch
):
continue
pool
=
MyPool
(
processes
=
n
)
results
=
pool
.
map
(
execute_job
,
bunch
)
pool
.
close
()
pool
.
join
()
if
len
(
fails
):
print
()
print
(
"Some jobs failed! :"
)
print
()
for
j
in
fails
:
print
(
j
.
cmd_
)
else
:
print
()
print
(
"Computations ran successfully."
)
print
()
# ================= Statistics (without pseudoknots) ========================
...
...
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