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