if VERBOSE >= 1:
print fragment
# Check whether a reference exists at all
ref_fn = patient.get_reference_filename(fragment)
if not os.path.isfile(ref_fn):
print 'ERROR: reference for fragment', fragment, 'not found!'
continue
elif VERBOSE >= 3:
print 'OK: reference file found'
refseq = SeqIO.read(ref_fn, 'fasta')
# Check whether the consensus from the first sample is similar to
# the reference
for i, sample in enumerate(patient.itersamples()):
if os.path.isfile(sample.get_consensus_filename(fragment)):
sample_init_seq = sample.get_consensus(fragment)
if (VERBOSE >= 1) and (i != 0):
print 'Consensus from initial sample missing, taking time point',
print 'n', i, '(start from zero)'
break
check = check_similarity_initial_sample(refseq, sample_init_seq, fragment,
VERBOSE=VERBOSE)
if not check:
if not use_force:
sys.exit()
# Get the specific fragment for this consensus
# NOTE: we only recently started hiding the frag spec in the reference name
if VERBOSE >= 1:
print fragment
# Check whether a reference exists at all
ref_fn = patient.get_reference_filename(fragment)
if not os.path.isfile(ref_fn):
print 'ERROR: reference for fragment', fragment, 'not found!'
continue
elif VERBOSE >= 3:
print 'OK: reference file found'
refseq = SeqIO.read(ref_fn, 'fasta')
# Check whether the consensus from the first sample is similar to
# the reference
for i, sample in enumerate(patient.itersamples()):
if os.path.isfile(sample.get_consensus_filename(fragment)):
sample_init_seq = sample.get_consensus(fragment)
if (VERBOSE >= 1) and (i != 0):
print 'Consensus from initial sample missing, taking time point',
print 'n', i, '(start from zero)'
break
check = check_similarity_initial_sample(refseq,
sample_init_seq,
fragment,
VERBOSE=VERBOSE)
if not check:
if not use_force:
sys.exit()
