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'
