fragments = args.fragments
patients = load_patients()
for fragment in fragments:
if VERBOSE >= 1:
print fragment
refs = []
for pname, patient in patients.iterrows():
if VERBOSE >= 2:
print pname
patient = Patient(patient)
refs.append(patient.get_reference(fragment))
ali = align_muscle(*refs, sort=True)
# Check whether all references are complete (using the longest primers)
if VERBOSE >= 2:
print 'Check alignment'
alim = np.array(ali)
if (alim[:, :4] == '-').any():
raise ValueError('Gaps at the beginning of fragment found')
elif (alim[:, -4:] == '-').any():
raise ValueError('Gaps at the end of fragment found')
if VERBOSE >= 2:
print 'Save to file'
fn = get_reference_alignment_filename(fragment)
AlignIO.write(ali, fn, 'fasta')
patient = Patient(patient)
for region in regions:
if VERBOSE >= 1:
print patient.name, region
if VERBOSE >= 2:
print 'Get haplotype counts'
(hct, ind, seqs) = patient.get_region_count_trajectories(region,
VERBOSE=VERBOSE)
times = patient.times[ind]
if VERBOSE >= 2:
print 'Align sequences'
ali = align_muscle(*seqs, sort=True)
alim = np.array(ali)
if VERBOSE >= 2:
print 'Get distributions'
ds = get_distance_distributions(hct, alim, VERBOSE=VERBOSE)
data.append({'pname': pname, 'ds': ds, 't': times,
'region': region})
if use_plot:
for pname, patient in patients.iterrows():
patient = Patient(patient)
nrows = 1 + (len(regions) - 1) // 3
fragments = args.fragments
patients = load_patients()
for fragment in fragments:
if VERBOSE >= 1:
print fragment
refs = []
for pname, patient in patients.iterrows():
if VERBOSE >= 2:
print pname
patient = Patient(patient)
refs.append(patient.get_reference(fragment))
ali = align_muscle(*refs, sort=True)
# Check whether all references are complete (using the longest primers)
if VERBOSE >= 2:
print 'Check alignment'
alim = np.array(ali)
if (alim[:, :4] == '-').any():
raise ValueError('Gaps at the beginning of fragment found')
elif (alim[:, -4:] == '-').any():
raise ValueError('Gaps at the end of fragment found')
if VERBOSE >= 2:
print 'Save to file'
fn = get_reference_alignment_filename(fragment)
AlignIO.write(ali, fn, 'fasta')
