def initFromParam(cls, param, is_control, param_attr): import ChIPSeqReplicate import File cse = cls() cse.param = param cse.is_control = is_control ftgts = getattr(param, param_attr).split(',') cse.reps = [ ChIPSeqReplicate.initFromFastqFile(ffq) for ffq in ftgts ] for (i, rep) in enumerate(cse.reps): rep.param = param rep.index = i+1 rep.chipseqexp = cse tgt_fta = "%s/%s.tagAlign.gz" % (param.temp_dir, rep.name) rep.tagalign = File.initFromFullFileName(tgt_fta) if cse.is_control: frep0 = param.fchipseq_control_signals else: frep0 = param.fchipseq_target_signals cse.pooled_tagalign = File.initFromFullFileName(frep0) cse.peaks = File.initFromFullFileName(param.fall_chipseq_peaks) cse.final_peaks = File.initFromFullFileName(param.fidr_chipseq_peaks) return cse
def genChIPSeqSignalFilesFromBed(param): import ChIPSeqReplicate fbeds = param.chipseq_bed_files_multi_targets.split(',') for fbed in fbeds: csr = ChIPSeqReplicate.initFromBedFile(fbed) ta = csr.tagalign param.targetid2fchipseq_alignment[ta.basename] = ta.fullname