def __init__(self, *args, **kwargs):
'''Initialize a patient with all his samples'''
super(Patient, self).__init__(*args, **kwargs)
from hivwholeseq.patients.samples import load_samples_sequenced
samples = load_samples_sequenced(patients=[self.name])
self.samples = samples
type=int,
default=0,
help='Verbosity level [0-4]')
parser.add_argument('--save',
action='store_true',
help='Save the allele counts to file')
args = parser.parse_args()
pnames = args.patients
samplenames = args.samples
VERBOSE = args.verbose
use_save = args.save
fragments = ['F' + str(i + 1) for i in xrange(6)]
samples = load_samples_sequenced()
if pnames is not None:
samples = samples.loc[samples.patient.isin(pnames)]
elif samplenames is not None:
samples = samples.loc[samples.index.isin(samplenames)]
for samplename, sample in samples.iterrows():
sample = SamplePat(sample)
if VERBOSE >= 1:
print samplename
dist_hists = []
samples_seq = sample.get_sequenced_samples()
samples_seq = samples_seq.loc[samples_seq.PCR == 1]
for samplename_seq, sample_seq in samples_seq.iterrows():
sample_seq = SampleSeq(sample_seq)
pats_or_samples.add_argument('--samples', nargs='+',
help='Samples to map')
parser.add_argument('--verbose', type=int, default=0,
help='Verbosity level [0-4]')
parser.add_argument('--save', action='store_true',
help='Save the allele counts to file')
args = parser.parse_args()
pnames = args.patients
samplenames = args.samples
VERBOSE = args.verbose
use_save = args.save
fragments = ['F'+str(i+1) for i in xrange(6)]
samples = load_samples_sequenced()
if pnames is not None:
samples = samples.loc[samples.patient.isin(pnames)]
elif samplenames is not None:
samples = samples.loc[samples.index.isin(samplenames)]
for samplename, sample in samples.iterrows():
sample = SamplePat(sample)
if VERBOSE >= 1:
print samplename
dist_hists = []
samples_seq = sample.get_sequenced_samples()
samples_seq = samples_seq.loc[samples_seq.PCR == 1]
for samplename_seq, sample_seq in samples_seq.iterrows():
sample_seq = SampleSeq(sample_seq)
author: Fabio Zanini
date: 18/05/15
content: Get days since infection from dates.
'''
# Globals
import pandas as pd
from hivwholeseq.patients.patients import load_patients
from hivwholeseq.patients.samples import load_samples_sequenced, itersample
# Script
if __name__ == '__main__':
samples = load_samples_sequenced(include_empty=True)
patients = load_patients()
dsi = []
for samplename, sample in itersample(samples):
t = sample.date
t0 = patients.loc[sample.patient]['infect date best']
dt = (t - t0).days
dsi.append({'sample': samplename,
'dsi': dt,
})
dsi = pd.DataFrame(dsi).set_index('sample')
print dsi
def __init__(self, *args, **kwargs):
'''Initialize a patient with all his samples'''
super(Patient, self).__init__(*args, **kwargs)
from hivwholeseq.patients.samples import load_samples_sequenced
samples = load_samples_sequenced(patients=[self.name])
self.samples = samples