deltamax=deltamax) consm = np.fromstring(cons, 'S1') if VERBOSE >= 2: print 'Reference length:', len_reference, 'consensus:', len(cons), if len_reference != len(cons): from seqanpy import align_local (score, ali1, ali2) = align_local(''.join(refseq), cons) alim1 = np.fromstring(ali1, 'S1') alim2 = np.fromstring(ali2, 'S1') n_diff = (alim1 != alim2).sum() print 'overlap', len(alim1), 'n diffs.', n_diff else: n_diff = (refm != consm).sum() print 'n diffs.', n_diff if save_to_file: if VERBOSE >= 2: print 'Save to file' fn_out = sample.get_consensus_filename(fragment, PCR=PCR) consrec = SeqRecord(Seq(cons, ambiguous_dna), id=samplename+'_consensus', name=samplename+'_consensus', description=samplename+', consensus', ) SeqIO.write(consrec, fn_out, 'fasta') if VERBOSE == 1: print ''
if VERBOSE >= 2: print 'Reference length:', len_reference, 'consensus:', len( cons), if len_reference != len(cons): from seqanpy import align_local (score, ali1, ali2) = align_local(''.join(refseq), cons) alim1 = np.fromstring(ali1, 'S1') alim2 = np.fromstring(ali2, 'S1') n_diff = (alim1 != alim2).sum() print 'overlap', len(alim1), 'n diffs.', n_diff else: n_diff = (refm != consm).sum() print 'n diffs.', n_diff if save_to_file: if VERBOSE >= 2: print 'Save to file' fn_out = sample.get_consensus_filename(fragment, PCR=PCR) consrec = SeqRecord( Seq(cons, ambiguous_dna), id=samplename + '_consensus', name=samplename + '_consensus', description=samplename + ', consensus', ) SeqIO.write(consrec, fn_out, 'fasta') if VERBOSE == 1: print ''
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, VERBOSE=VERBOSE) if len(consensus) < 8800: print 'WARNING: the consensus looks too short!' if use_save: output_filename = sample_pat.get_consensus_filename('genomewide') SeqIO.write(consensus, output_filename, 'fasta') if VERBOSE >= 1: print 'Genomewide consensus written'
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, VERBOSE=VERBOSE) if len(consensus) < 8800: print 'WARNING: the consensus looks too short!' if use_save: output_filename = sample_pat.get_consensus_filename('genomewide') SeqIO.write(consensus, output_filename, 'fasta') if VERBOSE >= 1: print 'Genomewide consensus written'