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