default=0,
help='Verbosity level [0-3]')
parser.add_argument('--allele-frequencies',
action='store_true',
dest='afs',
help='Use allele frequencies')
parser.add_argument('--reads', type=int, default=0, help='Use reads')
args = parser.parse_args()
pname = args.patient
fragments = args.fragments
VERBOSE = args.verbose
use_af = args.afs
maxreads = args.reads
patient = load_patient(pname)
times = patient.times
if not fragments:
fragments = ['F' + str(i) for i in xrange(1, 7)]
if VERBOSE >= 3:
print 'fragments', fragments
if VERBOSE:
print pname
if use_af:
divs = []
for fragment in fragments:
aft_filename = get_allele_frequency_trajectories_filename(
help='Fragment to map (e.g. F1 genomewide genomewide_new)')
parser.add_argument('--verbose', type=int, default=0,
help='Verbosity level [0-3]')
parser.add_argument('--sample',
help='Use a specific sample (not the first time point) for the reference')
parser.add_argument('--repnumber', type=int, default=0,
help='Index of the sequenced sample within that patient sample')
args = parser.parse_args()
pname = args.patient
fragments = args.fragments
VERBOSE = args.verbose
repn = args.repnumber
samplename = args.sample
patient = load_patient(pname)
patient.discard_nonsequenced_samples()
mkdirs(get_initial_reference_foldername(pname))
if not fragments:
fragments = ['F'+str(i) for i in xrange(1, 7)]
if VERBOSE >= 3:
print 'fragments', fragments
if samplename is None:
sample = SamplePat(patient.samples.iloc[samplen])
else:
sample = load_sample_sequenced(samplename)
for fragment in fragments: