if not os.path.isfile(bamfilename): continue # if check_already_decontaminated(sample, fragment, PCR_sample): # continue fork_self(samplename, fragment, VERBOSE=VERBOSE, maxreads=maxreads, summary=summary, PCR=PCR_sample) sys.exit() for fragment in fragments: consensi = {refname: "".join(load_custom_reference(refname + "_" + fragment)) for refname in refnames} for samplename, sample in samples.iterrows(): sample = SamplePat(sample) try: consensi[samplename] = sample.get_consensus(fragment, PCR=1) except IOError: print samplename, "file not found" continue for samplename, sample in samples_focal.iterrows(): sample = SamplePat(sample) pname = sample.patient if PCR is None: PCRs_sample = (1, 2) else: PCRs_sample = [PCR] for PCR_sample in PCRs_sample: bamfilename = sample.get_mapped_filtered_filename(fragment, PCR=PCR_sample, decontaminated=False)
VERBOSE=VERBOSE, maxreads=maxreads, summary=summary, PCR=PCR_sample) sys.exit() for fragment in fragments: consensi = { refname: ''.join(load_custom_reference(refname + '_' + fragment)) for refname in refnames } for samplename, sample in samples.iterrows(): sample = SamplePat(sample) try: consensi[samplename] = sample.get_consensus(fragment, PCR=1) except IOError: print samplename, 'file not found' continue for samplename, sample in samples_focal.iterrows(): sample = SamplePat(sample) pname = sample.patient if PCR is None: PCRs_sample = (1, 2) else: PCRs_sample = [PCR] for PCR_sample in PCRs_sample: bamfilename = sample.get_mapped_filtered_filename(
samples_pat = samples_pat.loc[samples_pat.index.isin(samplenames)] if VERBOSE >= 2: print 'samples', samples_pat.index.tolist() consensi = [] for samplename_pat, sample_pat in samples_pat.iterrows(): sample_pat = SamplePat(sample_pat) if VERBOSE >= 1: print sample_pat.name, consensi_pat = {} try: for i in xrange(6): fragment = 'F'+str(i+1) consensi_pat[fragment] = sample_pat.get_consensus(fragment) except IOError: if VERBOSE >= 1: print 'warning: some consensus not found: skipping' continue except ValueError: if VERBOSE >= 1: print 'warning: some consensus is not clean (e.g. contamination): skipping' continue if VERBOSE >= 1: print 'ok: all 6 consensi found' consensus = merge_fragments(consensi_pat, name=sample_pat.patient,
samples_pat = samples_pat.loc[samples_pat.index.isin(samplenames)] if VERBOSE >= 2: print 'samples', samples_pat.index.tolist() consensi = [] for samplename_pat, sample_pat in samples_pat.iterrows(): sample_pat = SamplePat(sample_pat) if VERBOSE >= 1: print sample_pat.name, consensi_pat = {} try: for i in xrange(6): fragment = 'F' + str(i + 1) consensi_pat[fragment] = sample_pat.get_consensus(fragment) except IOError: if VERBOSE >= 1: print 'warning: some consensus not found: skipping' continue except ValueError: if VERBOSE >= 1: print 'warning: some consensus is not clean (e.g. contamination): skipping' continue if VERBOSE >= 1: print 'ok: all 6 consensi found' consensus = merge_fragments(consensi_pat,