def get_subtype_reference_alignment_consensus(region, subtype='B', refname='HXB2', type='nuc', VERBOSE=0): '''Get filename of consensus of subtype reference alignment''' from Bio import SeqIO from hivwholeseq.cross_sectional.filenames import ( get_subtype_reference_alignment_consensus_filename) fn = get_subtype_reference_alignment_consensus_filename(region, subtype=subtype, refname=refname, type=type, VERBOSE=VERBOSE) return SeqIO.read(fn, 'fasta')
VERBOSE=VERBOSE) afs = np.load(fn_in) if VERBOSE >= 2: print 'Calculate consensus' consm = alphabet[afs[:5].argmax(axis=0)] consrec = SeqRecord(Seq(''.join(consm), alphabet_bio), id='consensus_subtype'+subtype+'_refto_'+refname, name='consensus_subtype'+subtype+'_refto_'+refname, description=('Consensus of subtype '+subtype+ ' reference alignment to '+refname), ) if VERBOSE >= 2: print 'Save to file' fn_out = get_subtype_reference_alignment_consensus_filename(region, subtype=subtype, refname=refname, type=alitype, VERBOSE=VERBOSE) SeqIO.write(consrec, fn_out, 'fasta') else: consrec = get_subtype_reference_alignment_consensus(region, subtype=subtype, refname=refname, type=alitype, VERBOSE=VERBOSE)
if VERBOSE >= 2: print 'Calculate consensus' consm = alphabet[afs[:5].argmax(axis=0)] consrec = SeqRecord( Seq(''.join(consm), alphabet_bio), id='consensus_subtype' + subtype + '_refto_' + refname, name='consensus_subtype' + subtype + '_refto_' + refname, description=('Consensus of subtype ' + subtype + ' reference alignment to ' + refname), ) if VERBOSE >= 2: print 'Save to file' fn_out = get_subtype_reference_alignment_consensus_filename( region, subtype=subtype, refname=refname, type=alitype, VERBOSE=VERBOSE) SeqIO.write(consrec, fn_out, 'fasta') else: consrec = get_subtype_reference_alignment_consensus( region, subtype=subtype, refname=refname, type=alitype, VERBOSE=VERBOSE)