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)
data_folder = sample_seq.seqrun_folder
adaID = sample_seq.adapter
for fragment in fragments:
try:
dist_hist = get_distance_histogram(data_folder,
adaID,
fragment,
VERBOSE=VERBOSE)
except IOError:
continue
dist_hists.append((samplename_seq, fragment, dist_hist))
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)
data_folder = sample_seq.seqrun_folder
adaID = sample_seq.adapter
for fragment in fragments:
try:
dist_hist = get_distance_histogram(data_folder, adaID, fragment,
VERBOSE=VERBOSE)
except IOError:
continue
dist_hists.append((samplename_seq, fragment, dist_hist))
dist_hists.sort(key=itemgetter(1))
