print '' if submit: fork_self(samplename, fragment, VERBOSE=VERBOSE, PCR=PCR, block_len=block_len, n_reads_per_ali=n_reads_per_ali) continue sample = SamplePat(sample) pname = sample.patient refseq = SeqIO.read(get_initial_reference_filename(pname, fragment), 'fasta') refm = np.array(refseq) len_reference = len(refseq) # NOTE: we need consensi to decontaminate, so bamfilename = sample.get_mapped_filtered_filename(fragment, PCR=PCR, decontaminated=(not use_raw_reads)) if not os.path.isfile(bamfilename): continue if VERBOSE >= 1: print 'PCR', PCR, if VERBOSE >= 2: print '' cons = build_consensus(bamfilename, len_reference, VERBOSE=VERBOSE, block_len=block_len, reads_per_alignment=n_reads_per_ali, deltamax=deltamax) consm = np.fromstring(cons, 'S1')
if not fragments: fragments = ['F' + str(i) for i in xrange(1, 7)] if VERBOSE >= 3: print 'fragments', fragments if submit: for fragment in fragments: for samplename, sample in samples_focal.iterrows(): sample = SamplePat(sample) 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) 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()
if not fragments: fragments = ["F" + str(i) for i in xrange(1, 7)] if VERBOSE >= 3: print "fragments", fragments if submit: for fragment in fragments: for samplename, sample in samples_focal.iterrows(): sample = SamplePat(sample) 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) 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:
fragment, VERBOSE=VERBOSE, PCR=PCR, block_len=block_len, n_reads_per_ali=n_reads_per_ali) continue sample = SamplePat(sample) pname = sample.patient refseq = SeqIO.read( get_initial_reference_filename(pname, fragment), 'fasta') refm = np.array(refseq) len_reference = len(refseq) # NOTE: we need consensi to decontaminate, so bamfilename = sample.get_mapped_filtered_filename( fragment, PCR=PCR, decontaminated=(not use_raw_reads)) if not os.path.isfile(bamfilename): continue if VERBOSE >= 1: print 'PCR', PCR, if VERBOSE >= 2: print '' cons = build_consensus(bamfilename, len_reference, VERBOSE=VERBOSE, block_len=block_len, reads_per_alignment=n_reads_per_ali, deltamax=deltamax) consm = np.fromstring(cons, 'S1')