def sample_pat(self): '''Patient sample of this sequencing sample''' if self._sample_pat is None: from hivwholeseq.patients.patients import load_samples_sequenced as lssp from hivwholeseq.patients.patients import SamplePat self._sample_pat = SamplePat(lssp(include_wrong=True).loc[self['patient sample']]) return self._sample_pat
def sample_pat(self): '''Patient sample of this sequencing sample''' if self._sample_pat is None: from hivwholeseq.patients.patients import load_samples_sequenced as lssp from hivwholeseq.patients.patients import SamplePat self._sample_pat = SamplePat( lssp(include_wrong=True).loc[self['patient sample']]) return self._sample_pat
action='store_true', help='Execute the script in parallel on the cluster') args = parser.parse_args() seq_runs = args.runs adaIDs = args.adaIDs use_pats = args.use_pats use_interactive = args.interactive detail = args.detail submit = args.submit if submit: fork_self(seq_runs, adaIDs=adaIDs, pats=use_pats, detail=detail) sys.exit() samples_pat = lssp(include_wrong=True) samples = lss() samples = samples.loc[samples['seq run'].isin(seq_runs)] if adaIDs is not None: samples = samples.loc[samples.adapter.isin(adaIDs)] if len(seq_runs) >= 2: samples.sort(columns=['patient sample', 'seq run'], inplace=True) for isa, (samplename, sample) in enumerate(samples.iterrows()): sample = SampleSeq(sample) print sample.name, 'seq:', sample['seq run'], sample.adapter, if sample['patient sample'] == 'nan': print 'not a patient sample', if use_pats:
samplenames = args.samples fragments = args.fragments submit = args.submit VERBOSE = args.verbose threads = args.threads n_pairs = args.maxreads skip_hash = args.skiphash summary = args.summary only_chunks = args.chunks if seq_runs is not None: samples_seq = lss() samples_seq = samples_seq.loc[samples_seq['seq run'].isin(seq_runs)] elif pnames is not None: samples_pat = lssp() samples_seq = [] for pname in pnames: patient = load_patient(pname) patient.discard_nonsequenced_samples() for samplename_pat, sample_pat in patient.samples.iterrows(): samples_seq.append(sample_pat['samples seq']) samples_seq = pd.concat(samples_seq) else: samples_pat = lssp() samples_seq = lss() ind = samples_pat.index.isin(samplenames) if ind.sum(): samplenames_pat = samples_pat.index[ind] samples_seq = samples_seq.loc[samples_seq['patient sample'].isin(
"--no-summary", action="store_false", dest="summary", help="Do not save results in a summary file" ) parser.add_argument("--submit", action="store_true", help="Execute the script in parallel on the cluster") parser.add_argument("--PCR", type=int, default=1, help="Analyze only reads from this PCR (e.g. 1)") args = parser.parse_args() pnames = args.patients samplenames = args.samples fragments = args.fragments submit = args.submit VERBOSE = args.verbose maxreads = args.maxreads summary = args.summary PCR = args.PCR samples = lssp() if pnames is not None: samples_focal = samples.loc[samples.patient.isin(pnames)] elif samplenames is not None: samples_focal = samples.loc[samples.index.isin(samplenames)] else: samples_focal = samples if VERBOSE >= 2: print "samples", samples_focal.index.tolist() if not fragments: fragments = ["F" + str(i) for i in xrange(1, 7)] if VERBOSE >= 3: print "fragments", fragments
pats_or_samples.add_argument('--patients', nargs='+', help='Patient to analyze') pats_or_samples.add_argument('--samples', nargs='+', help='Samples to map') parser.add_argument('--verbose', type=int, default=0, help='Verbosity level [0-3]') parser.add_argument('--save', action='store_true', help='Save genomewide consensi to file') args = parser.parse_args() pnames = args.patients samplenames = args.samples VERBOSE = args.verbose use_save = args.save samples_pat = lssp() if pnames is not None: samples_pat = samples_pat.loc[samples_pat.patient.isin(pnames)] elif samplenames is not None: samples_pat = samples_pat.loc[samples_pat.index.isin(samplenames)] if VERBOSE >= 2: print 'samples', samples_pat.index.tolist() consensi = [] for samplename_pat, sample_pat in samples_pat.iterrows(): sample_pat = SamplePat(sample_pat) if VERBOSE >= 1: print sample_pat.name, consensi_pat = {}
parser.add_argument('--PCR', type=int, default=1, help='Analyze only reads from this PCR (e.g. 1)') args = parser.parse_args() pnames = args.patients samplenames = args.samples fragments = args.fragments submit = args.submit VERBOSE = args.verbose maxreads = args.maxreads summary = args.summary PCR = args.PCR samples = lssp() if pnames is not None: samples_focal = samples.loc[samples.patient.isin(pnames)] elif samplenames is not None: samples_focal = samples.loc[samples.index.isin(samplenames)] else: samples_focal = samples if VERBOSE >= 2: print 'samples', samples_focal.index.tolist() if not fragments: fragments = ['F' + str(i) for i in xrange(1, 7)] if VERBOSE >= 3: print 'fragments', fragments