def dataProvider_testDepends(self):
pDepends1 = Proc()
pDepends2 = Proc()
pDepends3 = Proc()
pDepends4 = Proc()
pDepends5 = Proc()
aggr = Aggr(pDepends1, pDepends2, pDepends3)
aggr.starts = 'pDepends1, pDepends2'
aggr.depends = [aggr.pDepends2, aggr.pDepends3]
yield aggr, [[aggr.pDepends2], [aggr.pDepends3]]
aggr1 = Aggr(pDepends1, pDepends2, pDepends3, pDepends4, pDepends5)
aggr1.starts = 'pDepends1'
aggr1[:1].depends = [['pDepends3', 'pDepends5']]
yield aggr1, [[aggr1.pDepends3, aggr1.pDepends5]]
def dataProvider_testSetattr(self):
pSetattra = Proc()
pSetattra.args.a = Box()
pSetattrb = Proc()
pSetattrb.args.a = Box()
pSetattrc = Proc()
pSetattrc.args.a = Box(b=1)
pSetattrd = Proc()
pSetattre = Proc()
aggr = Aggr(pSetattra, pSetattrb, pSetattrc, pSetattrd, pSetattre)
aggr.delegate('forks', 'pSetattrb')
aggr.delegate('tag', 'ends')
yield aggr, 'forks', 10, [1, 10, 1, 1, 1]
yield aggr, 'tag', 't', [
aggr.pSetattra.tag, aggr.pSetattra.tag, aggr.pSetattra.tag,
aggr.pSetattra.tag, 't'
]
# depends and input
aggr.starts = 'pSetattra, pSetattrb'
yield aggr, 'depends', ['pSetattrc', 'pSetattrd'], [[aggr.pSetattrc],
[aggr.pSetattrd],
[aggr.pSetattrb],
[aggr.pSetattrc],
[aggr.pSetattrd]]
yield aggr, 'depends2', ['pSetattrc', 'pSetattrd'
], [[aggr.pSetattrc, aggr.pSetattrd],
[aggr.pSetattrc, aggr.pSetattrd],
[aggr.pSetattrb], [aggr.pSetattrc],
[aggr.pSetattrd]]
aggr1 = Aggr(pSetattra, pSetattrb, pSetattrc)
aggr1.delegate('errntry', 'pSetattra, pSetattrb')
aggr1.delegate('args.a', 'pSetattrb')
yield aggr1, 'errntry', 8, [8, 8, 3]
def dataProvider_testShowAllRoutes(self):
'''
/ p3 --- \
p1 -- p2 \ / p8
\ \ p4 \ p7
p10 p6 / \ p9
p5 /
'''
pShowAllRoutes1 = Proc()
pShowAllRoutes2 = Proc()
pShowAllRoutes3 = Proc()
pShowAllRoutes4 = Proc()
pShowAllRoutes5 = Proc()
pShowAllRoutes6 = Proc()
pShowAllRoutes7 = Proc()
pShowAllRoutes8 = Proc()
pShowAllRoutes9 = Proc()
pShowAllRoutes10 = Proc()
pShowAllRoutes3.depends = pShowAllRoutes2
pShowAllRoutes6.depends = pShowAllRoutes4, pShowAllRoutes5
pShowAllRoutes3.depends = pShowAllRoutes2
pShowAllRoutes4.depends = pShowAllRoutes2
pShowAllRoutes2.depends = pShowAllRoutes1
pShowAllRoutes10.depends = pShowAllRoutes1
aAggr = Aggr(pShowAllRoutes7, pShowAllRoutes8, pShowAllRoutes9)
aAggr.starts = [aAggr.pShowAllRoutes7]
aAggr.pShowAllRoutes8.depends = aAggr.pShowAllRoutes7
aAggr.pShowAllRoutes9.depends = aAggr.pShowAllRoutes7
aAggr.depends2 = [pShowAllRoutes3, pShowAllRoutes6]
yield [pShowAllRoutes1, pShowAllRoutes5], [
'DEBUG', '* pShowAllRoutes1 -> pShowAllRoutes10',
'pShowAllRoutes1 -> pShowAllRoutes2 -> pShowAllRoutes3 -> [aAggr]',
'* pShowAllRoutes1 -> pShowAllRoutes2 -> pShowAllRoutes4 -> pShowAllRoutes6 -> [aAggr]',
'* pShowAllRoutes5 -> pShowAllRoutes6 -> [aAggr]'
]
def dataProvider_testSetattr(self):
pSetattra = Proc()
pSetattra.args.a = Box()
pSetattrb = Proc()
pSetattrb.args.a = Box()
pSetattrc = Proc()
pSetattrc.args.a = Box(b=1)
pSetattrd = Proc()
pSetattre = Proc()
aggr = Aggr(pSetattra, pSetattrb, pSetattrc, pSetattrd, pSetattre)
aggr.delegate('forks', 'pSetattrb')
aggr.delegate('tag', 'ends')
proxy = _Proxy(aggr, check = True)
yield proxy, 'forks', 10, [1, 10, 1, 1, 1]
yield proxy, 'tag', 't', [aggr.pSetattra.tag, aggr.pSetattra.tag, aggr.pSetattra.tag, aggr.pSetattra.tag, 't']
# depends and input
aggr.starts = 'pSetattra, pSetattrb'
yield proxy, 'depends', ['pSetattrc', 'pSetattrd'], [[aggr.pSetattrc], [aggr.pSetattrd], [aggr.pSetattrb], [aggr.pSetattrc], [aggr.pSetattrd]]
yield proxy, 'depends2', ['pSetattrc', 'pSetattrd'], [[aggr.pSetattrc, aggr.pSetattrd], [aggr.pSetattrc, aggr.pSetattrd], [aggr.pSetattrb], [aggr.pSetattrc], [aggr.pSetattrd]]
aggr1 = Aggr(pSetattra, pSetattrb, pSetattrc)
aggr1.delegate('args.a.b', 'pSetattra, pSetattrb')
aggr1.delegate('args.a', 'pSetattrb')
proxy1 = _Proxy(aggr1, prefix = ['args', 'a'], check = True)
yield proxy1, 'b', 3, [3, 3, 1]
def dataProvider_testDelStart(self):
p1 = Proc()
p2 = Proc()
p3 = Proc()
aggr = Aggr(p1, p2, p3, depends=False)
aggr.starts = 'p1, p2'
yield aggr, [aggr.p1], [aggr.p2]
yield aggr, ['p1, p2'], []
def dataProvider_testDepends2(self):
pDepends21 = Proc()
pDepends22 = Proc()
pDepends23 = Proc()
pDepends24 = Proc()
pDepends25 = Proc()
aggr = Aggr(pDepends21, pDepends22, pDepends23)
aggr.starts = [pDepends21, pDepends22]
yield aggr, [pDepends24, pDepends25]
def dataProvider_testFlowchart(self):
'''
/ p3 --- \
p1 -- p2 \ / p8
\ \ p4 \ p7
p10 p6 / \ p9
p5 /
'''
pFlowchart1 = Proc()
pFlowchart2 = Proc()
pFlowchart3 = Proc()
pFlowchart4 = Proc()
pFlowchart5 = Proc()
pFlowchart6 = Proc()
pFlowchart7 = Proc()
pFlowchart8 = Proc()
pFlowchart9 = Proc()
pFlowchart10 = Proc()
pFlowchart3.depends = pFlowchart2
pFlowchart6.depends = pFlowchart4, pFlowchart5
pFlowchart3.depends = pFlowchart2
pFlowchart4.depends = pFlowchart2
pFlowchart2.depends = pFlowchart1
pFlowchart10.depends = pFlowchart1
aAggr = Aggr(pFlowchart7, pFlowchart8, pFlowchart9)
aAggr.starts = [aAggr.pFlowchart7]
aAggr.pFlowchart8.depends = aAggr.pFlowchart7
aAggr.pFlowchart9.depends = aAggr.pFlowchart7
aAggr.depends2 = [pFlowchart3, pFlowchart6]
dotfile = path.join(self.testdir, 'test.dot')
fcfile = path.join(self.testdir, 'test.svg')
yield [pFlowchart1, pFlowchart5], fcfile, dotfile, [
'DEBUG',
'* pFlowchart1 -> pFlowchart10',
'pFlowchart1 -> pFlowchart2 -> pFlowchart3 -> [aAggr]',
'* pFlowchart1 -> pFlowchart2 -> pFlowchart4 -> pFlowchart6 -> [aAggr]',
'* pFlowchart5 -> pFlowchart6 -> [aAggr]',
'INFO',
'Flowchart file saved to: %s' % fcfile,
'DOT file saved to: %s' % dotfile,
]
yield [pFlowchart1, pFlowchart5], fcfile, None, [
'DEBUG',
'* pFlowchart1 -> pFlowchart10',
'pFlowchart1 -> pFlowchart2 -> pFlowchart3 -> [aAggr]',
'* pFlowchart1 -> pFlowchart2 -> pFlowchart4 -> pFlowchart6 -> [aAggr]',
'* pFlowchart5 -> pFlowchart6 -> [aAggr]',
'INFO',
'Flowchart file saved to: %s' % fcfile,
'DOT file saved to: %s' % dotfile,
]
def dataProvider_testCopy(self):
pCopy1 = Proc()
pCopy2 = Proc()
pCopy3 = Proc()
pCopy4 = Proc()
aggr = Aggr(pCopy1, pCopy2, pCopy3)
aggr.depends = [pCopy4]
yield aggr, 'newtag', True, 'newid'
yield aggr, None, True, None
yield aggr, None, False, None
yield aggr, aggr.pCopy1.tag, False, None, False, False, AggrCopyError, 'Cannot copy process with same id and tag: \'pCopy1.%s\'' % aggr.pCopy1.tag
aggr1 = Aggr(pCopy1, pCopy2, pCopy3, depends=False)
aggr1.starts = [aggr1.pCopy1, aggr1.pCopy2]
aggr1.pCopy3.depends = aggr1.starts
aggr1.module('qc', lambda a: True, lambda a: False)
yield aggr1, None, True, None, True, True
def dataProvider_testAny2Procs(self):
pAny2Procs1 = Proc()
pAny2Procs2 = Proc()
pAny2Procs3 = Proc()
pAny2Procs4 = Proc()
pAny2Procs51 = Proc(tag='51', id='pAny2Procs5')
pAny2Procs52 = Proc(tag='52', id='pAny2Procs5')
pAny2Procs6 = Proc()
pAny2Procs7 = Proc()
aAggr = Aggr(pAny2Procs6, pAny2Procs7)
aAggr.starts = [aAggr.pAny2Procs6, aAggr.pAny2Procs7]
yield [pAny2Procs1], [pAny2Procs1]
yield ['abc'], [], PyPPLProcFindError, 'Failed to find process'
yield [aAggr], [aAggr.pAny2Procs6, aAggr.pAny2Procs7]
yield ['pAny2Procs5'], [pAny2Procs51, pAny2Procs52]
yield ['pAny2Procs5.51'], [pAny2Procs51]
yield ['pAny2Procs1.notag'], [pAny2Procs1]
yield ['pAny2Procs5', aAggr, [pAny2Procs2, 'pAny2Procs1.notag']], [
pAny2Procs51, pAny2Procs52, pAny2Procs1, pAny2Procs2,
aAggr.pAny2Procs6, aAggr.pAny2Procs7
]
pSimRead,
pBedGetfasta,
pMotifScan,
depends = False
)
# defaults
aTfbsTfP.pPromoters.runner = 'local'
delegate
aTfbsTfP.delegate('args.up' , 'pPromoters')
aTfbsTfP.delegate('args.down' , 'pPromoters')
aTfbsTfP.delegate('args.genome' , 'pPromoters')
aTfbsTfP.delegate('args.ref' , 'pBedGetfasta')
aTfbsTfP.delegate('args.pval' , 'pMotifScan')
aTfbsTfP.delegate('args.tfmotifs', 'pMotifScan')
# depends
aTfbsTfP.starts = aTfbsTfP.pTFs, aTfbsTfP.pPromoters, aTfbsTfP.pTFList
aTfbsTfP.ends = aTfbsTfP.pMotifScan
aTfbsTfP.pMotifScan.depends = aTfbsTfP.pSimRead, aTfbsTfP.pBedGetfasta
aTfbsTfP.pBedGetfasta.depends = aTfbsTfP.pPromoters
aTfbsTfP.pSimRead.depends = aTfbsTfP.pTFList, aTfbsTfP.pTFs
# input
aTfbsTfP.pTFList.input = [params.tflist.value]
# input size of either pTFs or pTFList should be 1
aTfbsTfP.pSimRead.input = lambda ch1, ch2: [ch1.repRow(l).cbind(ch2.repRow(l)).flatten() for l in [max(ch1.length(), ch2.length())]]
aTfbsTfP.pMotifScan.input = lambda ch1, ch2: [ch1.repRow(l).cbind(ch2.repRow(l)) for l in [max(ch1.length(), ch2.length())]][0]
# args
aTfbsTfP.pBedGetfasta.args.params.name = True
aTfbsTfP.pTFList.args.params.k = 2
aTfbsTfP.pSimRead.args.match = 'lambda line1, line2: -1 if line1[1] == line2[0] else 0 if line1[1] < line2[0] else 1'
aTfbsTfP.pSimRead.args.do = 'lambda line1, line2: fout.write("\\t".join(line1) + "\\n")'
def testSetGetAttr(self):
pGetAttr1 = Proc()
pGetAttr2 = Proc()
pGetAttr3 = Proc()
pGetAttr4 = Proc()
pGetAttr5 = Proc()
pGetAttr1.args.params = Box(inopts=Box())
pGetAttr2.args.params = Box(inopts=Box())
pGetAttr3.args.params = Box(inopts=Box())
pGetAttr4.args.params = Box(inopts=Box())
pGetAttr5.args.params = Box(inopts=Box())
aggr = Aggr(pGetAttr1,
pGetAttr2,
pGetAttr3,
pGetAttr4,
pGetAttr5,
depends=False)
# nothing delegated yet
self.assertDictEqual(
{
'input': ['starts'],
'depends': ['starts'],
'exdir': ['ends'],
'exhow': ['ends'],
'expart': ['ends'],
'exow': ['ends']
}, aggr._delegates)
# but when starts and ends changed
aggr.starts = [aggr.pGetAttr1, aggr.pGetAttr2]
aggr.ends = [aggr.pGetAttr5]
self.assertDictEqual(
{
'input': ['starts'],
'depends': ['starts'],
'exdir': ['ends'],
'exhow': ['ends'],
'expart': ['ends'],
'exow': ['ends']
}, aggr._delegates)
# delegate a short attribute
aggr.delegate('forks', [aggr.pGetAttr2, aggr.pGetAttr3])
aggr.forks = 10
# only 2, 3 changed
self.assertListEqual([p.forks for p in aggr._procs.values()],
[1, 10, 10, 1, 1])
# change the specific procs
aggr['pGetAttr2', 'pGetAttr4'].forks = 5
self.assertListEqual([p.forks for p in aggr._procs.values()],
[1, 10, 10, 5, 1])
# fix an attribute
aggr.pGetAttr3.runner = 'dry'
aggr.runner = 'sge'
self.assertListEqual(
[p.config['runner'] for p in aggr._procs.values()],
['sge', 'sge', 'dry', 'sge', 'sge'])
# set input
self.assertRaises(AggrAttributeError, setattr, aggr, 'input', 1)
aggr.input = [1, 2]
self.assertListEqual([p.config['input'] for p in aggr._procs.values()],
[1, 2, '', '', ''])
# reverse it
aggr.input = ['', '']
aggr.input2 = [1, 2]
self.assertListEqual([p.config['input'] for p in aggr._procs.values()],
[[1, 2], [1, 2], '', '', ''])
aggr[3].input = 'i3'
self.assertListEqual([p.config['input'] for p in aggr._procs.values()],
[[1, 2], [1, 2], '', 'i3', ''])
# not suppose to do this
# aggr.input2[2] = ['a', 'b']
#self.assertListEqual([p.config['input'] for p in aggr._procs.values()], [[1,2], [1,2], ['a', 'b'], 'i3', ''])
# similar for depends
#self.assertRaises(AggrAttributeError, setattr, aggr, 'depends', 1)
aggr.depends = [pGetAttr1, pGetAttr2]
self.assertListEqual([p.depends for p in aggr._procs.values()],
[[pGetAttr1], [pGetAttr2], [], [], []])
# reverse it
aggr.depends = [[], []]
aggr.depends2 = [pGetAttr1, pGetAttr2]
self.assertListEqual(
[p.depends for p in aggr._procs.values()],
[[pGetAttr1, pGetAttr2], [pGetAttr1, pGetAttr2], [], [], []])
# set attributes of certain processes
aggr[0].args.params = Box(inopts=Box(a=1))
self.assertListEqual([p.args for p in aggr._procs.values()], [
Box(params=Box(inopts=Box(a=1))),
Box(params=Box(inopts=Box())),
Box(params=Box(inopts=Box())),
Box(params=Box(inopts=Box())),
Box(params=Box(inopts=Box())),
])
aggr[:2].args.params = Box(inopts=Box(b=1))
self.assertListEqual([p.args for p in aggr._procs.values()], [
Box(params=Box(inopts=Box(b=1))),
Box(params=Box(inopts=Box(b=1))),
Box(params=Box(inopts=Box())),
Box(params=Box(inopts=Box())),
Box(params=Box(inopts=Box())),
])
aggr[1, 2].args.params = Box(inopts=Box(c=1))
self.assertListEqual([p.args for p in aggr._procs.values()], [
Box(params=Box(inopts=Box(b=1))),
Box(params=Box(inopts=Box(c=1))),
Box(params=Box(inopts=Box(c=1))),
Box(params=Box(inopts=Box())),
Box(params=Box(inopts=Box())),
])
# using proc ids
aggr['pGetAttr1'].args.params = Box(inopts=Box(d=1))
self.assertListEqual([p.args for p in aggr._procs.values()], [
Box(params=Box(inopts=Box(d=1))),
Box(params=Box(inopts=Box(c=1))),
Box(params=Box(inopts=Box(c=1))),
Box(params=Box(inopts=Box())),
Box(params=Box(inopts=Box())),
])
aggr['pGetAttr1', 'pGetAttr3'].args.params = Box(inopts=Box(e=1))
self.assertListEqual([p.args for p in aggr._procs.values()], [
Box(params=Box(inopts=Box(e=1))),
Box(params=Box(inopts=Box(c=1))),
Box(params=Box(inopts=Box(e=1))),
Box(params=Box(inopts=Box())),
Box(params=Box(inopts=Box())),
])
aggr['pGetAttr1, pGetAttr3'].args.params = Box(inopts=Box(f=1))
self.assertListEqual([p.args for p in aggr._procs.values()], [
Box(params=Box(inopts=Box(f=1))),
Box(params=Box(inopts=Box(c=1))),
Box(params=Box(inopts=Box(f=1))),
Box(params=Box(inopts=Box())),
Box(params=Box(inopts=Box())),
])
aggr['starts'].args.params = Box(inopts=Box(g=1))
self.assertListEqual([p.args for p in aggr._procs.values()], [
Box(params=Box(inopts=Box(g=1))),
Box(params=Box(inopts=Box(g=1))),
Box(params=Box(inopts=Box(f=1))),
Box(params=Box(inopts=Box())),
Box(params=Box(inopts=Box())),
])
aggr['ends'].args.params = Box(inopts=Box(h=1))
self.assertListEqual([p.args for p in aggr._procs.values()], [
Box(params=Box(inopts=Box(g=1))),
Box(params=Box(inopts=Box(g=1))),
Box(params=Box(inopts=Box(f=1))),
Box(params=Box(inopts=Box())),
Box(params=Box(inopts=Box(h=1))),
])
aggr.delegate('args.params.inopts', 'pGetAttr3')
aggr.args['params'].inopts = Box(n=1)
self.assertListEqual([p.args for p in aggr._procs.values()], [
Box(params=Box(inopts=Box(g=1))),
Box(params=Box(inopts=Box(g=1))),
Box(params=Box(inopts=Box(n=1))),
Box(params=Box(inopts=Box())),
Box(params=Box(inopts=Box(h=1))),
])
aggr.args.params['inopts'] = Box(m=1)
self.assertListEqual([p.args for p in aggr._procs.values()], [
Box(params=Box(inopts=Box(g=1))),
Box(params=Box(inopts=Box(g=1))),
Box(params=Box(inopts=Box(m=1))),
Box(params=Box(inopts=Box())),
Box(params=Box(inopts=Box(h=1))),
])
aggr[0].args.params.inopts = Box(z=1)
# remeber at line 453, inopts refers to the same Box() object, so both pGetAttr1 and 3 will change
self.assertListEqual(
[p.args for p in aggr._procs.values()],
[
Box(params=Box(inopts=Box(z=1))),
Box(params=Box(inopts=Box(z=1))), # <-- not g
Box(params=Box(inopts=Box(m=1))),
Box(params=Box(inopts=Box())),
Box(params=Box(inopts=Box(h=1))),
])
aggr.args.params.inopts.cnames = True
self.assertListEqual(
[p.args.params.inopts for p in aggr._procs.values()], [
Box(z=1),
Box(z=1),
Box(m=1, cnames=True),
Box(),
Box(h=1),
])
# something undelegated
aggr.tag = 'abc'
self.assertListEqual([p.tag for p in aggr._procs.values()],
['abc'] * 5)
del aggr._delegates['args.params.inopts']
aggr.delegate('args', 'pGetAttr4')
aggr.args.params.inopts.rnames = True
self.assertListEqual(
[p.args.params.inopts for p in aggr._procs.values()], [
Box(z=1),
Box(z=1),
Box(m=1, cnames=True),
Box(rnames=True),
Box(h=1),
])
pCNVkitHeatmap, # all tumor samples , in: cnfiles , out: plots
pCNVkitReport, # each tumor sample , in: cnr, cns , out: reports
pCNVkit2Vcf, # each tumor sample , in: callcns , out: vcf,
depends=False)
# defaults
aBam2SCNV.pBamDir.runner = 'local'
aBam2SCNV.pSampleInfo.runner = 'local'
# delegates
aBam2SCNV.delegate('args.ref', 'pCNVkitPrepare, pCNVkitRef')
aBam2SCNV.delegate(
'args.cnvkit',
'pCNVkitRef, pCNVkitFix, pCNVkitSeg, pCNVkitCall, pCNVkitScatter, pCNVkitDiagram, pCNVkitHeatmap, pCNVkitReport, pCNVkit2Vcf'
)
aBam2SCNV.delegate('args.nthread', 'pCNVkitCov, pCNVkitSeg')
# depends
aBam2SCNV.starts = aBam2SCNV.pBamDir, aBam2SCNV.pSampleInfo
aBam2SCNV.ends = aBam2SCNV.pCNVkit2Vcf
aBam2SCNV.pCNVkitPrepare.depends = aBam2SCNV.pBamDir, aBam2SCNV.pSampleInfo
aBam2SCNV.pCNVkitCov.depends = aBam2SCNV.pBamDir, aBam2SCNV.pSampleInfo, aBam2SCNV.pCNVkitPrepare
aBam2SCNV.pCNNDir.depends = aBam2SCNV.pCNVkitCov
aBam2SCNV.pCNVkitRef.depends = aBam2SCNV.pCNNDir, aBam2SCNV.pSampleInfo
aBam2SCNV.pCNVkitFix.depends = aBam2SCNV.pCNNDir, aBam2SCNV.pSampleInfo, aBam2SCNV.pCNVkitRef
aBam2SCNV.pCNVkitSeg.depends = aBam2SCNV.pCNVkitFix
aBam2SCNV.pCNVkitCall.depends = aBam2SCNV.pCNVkitSeg
aBam2SCNV.pCNVkit2Vcf.depends = aBam2SCNV.pCNVkitCall
# input
aBam2SCNV.pCNVkitPrepare.input = lambda ch_bamdir, ch_saminfo: [
Channel.create(SampleInfo(ch_saminfo.get()).toChannel(ch_bamdir.get())).
unique().flatten()
]
aBam2SCNV.pCNVkitCov.input = lambda ch_bamdir, ch_saminfo, ch_target: \
aExpDir2Deg
@description:
From expfiles to degs with sample info file.
@depends:
```
pExprDir2Matrix[*] \
pRNASeqDEG[!]
pSampleInfo[*] /
```
"""
aExpDir2Deg = Aggr(pExprDir2Matrix,
pFile2Proc.copy(id='pSampleInfo'),
pRNASeqDEG,
depends=False)
# Dependences
aExpDir2Deg.starts = aExpDir2Deg.pExprDir2Matrix, aExpDir2Deg.pSampleInfo
aExpDir2Deg.ends = aExpDir2Deg.pRNASeqDEG
aExpDir2Deg.pRNASeqDEG.depends = aExpDir2Deg.pExprDir2Matrix, aExpDir2Deg.pSampleInfo
# Input
aExpDir2Deg.pRNASeqDEG.input = lambda ch1, ch2: \
ch1.colAt(0).repRow(ch2.length()).cbind(ch2.repRow(ch1.length()))
# Args
aExpDir2Deg.pExprDir2Matrix.args.boxplot = True
aExpDir2Deg.pExprDir2Matrix.args.heatmap = True
aExpDir2Deg.pExprDir2Matrix.args.histplot = True
aExpDir2Deg.pRNASeqDEG.args.maplot = True
aExpDir2Deg.pRNASeqDEG.args.heatmap = True
"""
@name:
aExpDir2DegGSEA
@description:
def dataProvider_testRun(self):
'''
/ p3 --- \
p1 -- p2 \ / p8
\ \ p4 \ p7
p10 p6 / \ p9
p5 /
'''
pRun0 = Proc()
pRun1 = pRun0.copy()
pRun2 = Proc()
pRun3 = Proc()
pRun4 = Proc()
pRun5 = Proc()
pRun6 = Proc()
pRun7 = Proc()
pRun8 = Proc()
pRun9 = Proc()
pRun10 = Proc()
pRun3.depends = pRun2
pRun6.depends = pRun4, pRun5
pRun3.depends = pRun2
pRun4.depends = pRun2
pRun2.depends = pRun1
pRun10.depends = pRun1
aAggr = Aggr(pRun7, pRun8, pRun9)
aAggr.starts = [aAggr.pRun7]
aAggr.pRun8.depends = aAggr.pRun7
aAggr.pRun9.depends = aAggr.pRun7
aAggr.depends2 = [pRun3, pRun6]
yield [pRun1, pRun5], 'profile', 'sge', [
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'pRun1 (pRun0): No description.',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'pRun2: No description.',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'pRun3: No description.',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'pRun4: No description.',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'pRun5: No description.',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'pRun6: No description.',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'pRun10: No description.',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'pRun7.5gPF@aAggr: No description.',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'pRun8.5gPF@aAggr: No description.',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
'pRun9.5gPF@aAggr: No description.',
'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~',
]
# pRun21 -> pRun22
# pRun23 -/
# \-> pRun24
pRun21 = Proc()
pRun23 = Proc()
pRun22 = Proc()
pRun22.depends = pRun21, pRun23
yield [pRun21], 'profile', 'local', [
"pRun22 won't run as path can't be reached: pRun22 <- pRun23"
]