def testModule(self):
pModule1 = Proc()
pModule2 = Proc()
pModule3 = Proc()
pModule4 = Proc()
pModule5 = Proc()
pModule6 = Proc()
aggr = Aggr(pModule1,
pModule2,
pModule3,
pModule4,
pModule5,
pModule6,
depends=False)
aggr.module('m1',
starts='pModule1, pModule2',
ends='pModule4',
depends={
'pModule3,': ['starts'],
'pModule4': 'pModule3'
},
ends_shared={'pModule4': 'm2'},
depends_shared={'pModule4': 'm2'})
aggr.module('m2',
starts='pModule3',
ends='pModule4, pModule6',
depends={'pModule4': 'pModule3'},
ends_shared={'pModule4': 'm1'},
depends_shared={'pModule4': 'm1'},
starts_shared={'pModule3': 'm1'})
self.assertEqual(aggr.starts, [])
self.assertEqual(aggr.ends, [])
self.assertEqual(aggr.pModule3.depends, [])
self.assertEqual(aggr.pModule4.depends, [])
aggr.on('m1')
self.assertEqual(aggr.starts, [aggr.pModule1, aggr.pModule2])
self.assertEqual(aggr.ends, [aggr.pModule4])
self.assertEqual(aggr.pModule3.depends, [aggr.pModule1, aggr.pModule2])
self.assertEqual(aggr.pModule4.depends, [aggr.pModule3])
aggr.off('m1')
self.assertEqual(aggr.starts, [])
self.assertEqual(aggr.ends, [])
self.assertEqual(aggr.pModule3.depends, [])
self.assertEqual(aggr.pModule4.depends, [])
aggr.on('m2')
self.assertEqual(aggr.starts, [aggr.pModule3])
self.assertEqual(aggr.ends, [aggr.pModule4, aggr.pModule6])
self.assertEqual(aggr.pModule4.depends, [aggr.pModule3])
aggr.off('m2')
self.assertEqual(aggr.starts, [])
self.assertEqual(aggr.ends, [])
self.assertEqual(aggr.pModule3.depends, [])
aggr.on('m1, m2')
aggr.off('m2')
self.assertEqual(aggr.starts,
[aggr.pModule1, aggr.pModule2, aggr.pModule3])
self.assertEqual(aggr.ends, [aggr.pModule4])
self.assertEqual(aggr.pModule3.depends, [aggr.pModule1, aggr.pModule2])
self.assertEqual(aggr.pModule4.depends, [aggr.pModule3])
aPrepareBam['pSam2Bam', ].depends = ['pFastq2Sam']
aPrepareBam['pBamRecal', ].depends = ['pSam2Bam']
# delegates
aPrepareBam.delegate('args.ref', 'pFastq2Sam, pBamRecal')
# args
aPrepareBam.pSam2Bam.args.markdup = True
# modules
aPrepareBam.module('ebam',
starts='pBam2Fastq',
depends={'pFastqTrim': 'pBam2Fastq'})
aPrepareBam.module('fastq', starts='pFastqTrim')
aPrepareBam.module('qc',
ends='pFastQC, pFastMC',
depends={'pFastQC, pFastMC': ['pFastqTrim'] * 2})
# inital modules
aPrepareBam.on('fastq')
"""
@name:
aBam2SCNV
@description:
Call CNV with paired control samples
@procs:
`pBamDir` : The directory with the bam files
`pSampleInfo` : The sample information
`pCNVkitPrepare`: Prepare the region/coverage file for CNV calling
`pCNVkitCov` : Get the coverage file for each bam file.
`pCNNDir` : Put all coverage file into a directory.
`pCNVkitRef` : Aggregate the reference cnn file from controls.
`pCNVkitFix` : Fix the coverage for each sample using the reference cnn file.
`pCNVkitSeg` : Segment the regions
`pCNVkitCall` : Call CNVs.
aCELDir2DEG.ends = 'pMArrayDEG'
aCELDir2DEG['pGMTFetcher'].input = ['KEGG_2016_gmt']
aCELDir2DEG['pMArrayDEG'].args.maplot = True
aCELDir2DEG['pMArrayDEG'].args.heatmap = True
aCELDir2DEG['pGMTFetcher'].args.header = False
# Depends
aCELDir2DEG['pMArrayDEG', ].depends = ['pCELDir2Matrix, pSampleInfo']
# Input adjustments
aCELDir2DEG['pGSEA'].input = lambda ch1, ch2, ch3: \
ch1.repRow(ch2.length() * ch3.length()) \
.cbind(ch2.repRow(ch1.length() * ch3.length())) \
.cbind(ch3.repRow(ch1.length() * ch2.length()))
aCELDir2DEG['pMArrayDEG'].input = lambda ch1, ch2: \
ch1.colAt(0).repRow(ch2.length()).cbind(ch2.repRow(ch1.length()))
# Configs
aCELDir2DEG.module('exprplot',
depends={'pExprPlot': 'pCELDir2Matrix'},
ends='pExprPlot')
aCELDir2DEG.module(
'gsea', 'pGMTFetcher', {
'pGSEA': 'pExprMat2GCT, pSampleinfo2CLS, pGMTFetcher',
'pExprMat2GCT': 'pCELDir2Matrix',
'pSampleinfo2CLS': 'pSampleInfo'
}, 'pGSEA')
aCELDir2DEG.module('enrichr',
depends={'pEnrichr': 'pMArrayDEG'},
ends='pEnrichr')
# Enable all functions
aCELDir2DEG.on()