def genChIPSeqSignalFilesFromReads(param):
import ChIPSeqExperiment
cse_target = ChIPSeqExperiment.initFromParam(param, 'multi-targets')
cse_target.getFastqEncoding()
cse_target.alignReadByBowtie()
param.chipseqexperiment_target = cse_target
for rep in cse_target.reps:
ta = rep.tagalign
param.targetid2fchipseq_alignment[ta.basename] = ta.fullname
def genChIPSeqPeakFileBySPPIDR(param):
import ChIPSeqExperiment
cse_target = ChIPSeqExperiment.initFromParam(param, 'target')
cse_target.getFastqEncoding()
cse_target.alignReadByBowtie()
cse_target.poolTagAlign()
param.chipseqexperiment_target = cse_target
if param.chipseq_control_read_files is not None:
cse_control = ChIPSeqExperiment.initFromParam(param, 'control')
cse_control.getFastqEncoding()
cse_control.alignReadByBowtie()
cse_control.poolTagAlign()
cse_target.callPeaksBySPP(cse_control.pooled_tagalign)
cse_target.getPeaksByIDR(cse_control.pooled_tagalign)
param.chipseq_peak_file = cse_target.final_peaks.fullname
param.chipseqexperiment_control = cse_control
else:
pass ## to-be-implemented, call peaks by MOSAiCS without ChIP-seq control
