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
