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
