patients = patients.loc[pnames]
for pname, patient in patients.iterrows():
patient = Patient(patient)
if VERBOSE >= 1:
print 'Patient:', patient.name
patient.discard_nonsequenced_samples()
for fragment in fragments:
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',
VERBOSE = args.verbose
pnames = args.patients
use_save = args.save
use_force = args.force
patients = load_patients()
if pnames is not None:
patients = patients.loc[patients.index.isin(pnames)]
for pname, patient in patients.iterrows():
patient = Patient(patient)
if VERBOSE:
print 'Patient:', patient.name
fn = patient.get_reference_filename('genomewide')
refseq = SeqIO.read(fn, 'fasta', alphabet=ambiguous_dna)
fragment_edges = get_edges_fragments(patient, VERBOSE=VERBOSE)
annotate_sequence(refseq, VERBOSE=VERBOSE,
additional_edges={'fragment': fragment_edges})
if VERBOSE >= 1:
for feature in refseq.features:
if feature.id[0] == 'F':
continue
print feature.id,
from hivwholeseq.utils.genome_info import genes
if feature.type in ('gene', 'protein'):
print feature.extract(refseq).seq.translate()
if not fragments:
fragments = ['F'+str(i) for i in xrange(1, 7)]
if VERBOSE >= 2:
print 'fragments', fragments
if use_recover:
for pname, patient in patients.iterrows():
print pname
patient = Patient(patient)
patient.discard_nonsequenced_samples()
for fragment in fragments:
if VERBOSE >= 1:
print fragment
fn = patient.get_reference_filename(fragment)
fn_old = fn.replace('.fasta', '_old.fasta')
if not os.path.isfile(fn_old):
print 'Old reference not found, skipping'
continue
shutil.copy(fn_old, fn)
os.chmod(fn, (stat.S_IRUSR | stat.S_IRGRP | stat.S_IROTH | \
stat.S_IWUSR))
os.chmod(fn_old, (stat.S_IRUSR | stat.S_IRGRP | stat.S_IROTH | \
stat.S_IWUSR))
os.remove(fn_old)
if VERBOSE >= 1:
print 'Old reference recovered and protection removed'
continue
sys.exit()
patients = patients.loc[pnames]
for pname, patient in patients.iterrows():
patient = Patient(patient)
if VERBOSE >= 1:
print 'Patient:', patient.name
patient.discard_nonsequenced_samples()
for fragment in fragments:
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',
VERBOSE = args.verbose
pnames = args.patients
use_save = args.save
use_force = args.force
patients = load_patients()
if pnames is not None:
patients = patients.loc[patients.index.isin(pnames)]
for pname, patient in patients.iterrows():
patient = Patient(patient)
if VERBOSE:
print 'Patient:', patient.name
fn = patient.get_reference_filename('genomewide')
refseq = SeqIO.read(fn, 'fasta', alphabet=ambiguous_dna)
fragment_edges = get_edges_fragments(patient, VERBOSE=VERBOSE)
annotate_sequence(refseq,
VERBOSE=VERBOSE,
additional_edges={'fragment': fragment_edges})
if VERBOSE >= 1:
for feature in refseq.features:
if feature.id[0] == 'F':
continue
print feature.id,
from hivwholeseq.utils.genome_info import genes
if feature.type in ('gene', 'protein'):
