def get_initial_allele_counts(self, fragment):
'''Get allele counts from the initial time point'''
import os
from hivwholeseq.patients.samples import SamplePat
for i in xrange(len(self.samples)):
sample = SamplePat(self.samples.iloc[i])
if os.path.isfile(sample.get_allele_counts_filename(fragment)):
return sample.get_allele_counts(fragment)
def get_initial_allele_counts(self, fragment):
'''Get allele counts from the initial time point'''
import os
from hivwholeseq.patients.samples import SamplePat
for i in xrange(len(self.samples)):
sample = SamplePat(self.samples.iloc[i])
if os.path.isfile(sample.get_allele_counts_filename(fragment)):
return sample.get_allele_counts(fragment)
if pnames is not None:
samples = samples.loc[samples.patient.isin(pnames)]
elif samplenames is not None:
samples = samples.loc[samples.index.isin(samplenames)]
if VERBOSE >= 2:
print 'samples', samples.index.tolist()
for region in regions:
for samplename, sample in samples.iterrows():
sample = SamplePat(sample)
if VERBOSE >= 1:
print region, samplename
count = sample.get_allele_counts(region, qual_min=qual_min)
if use_plot:
x = np.tile(np.arange(count.shape[1]), (count.shape[0], 1))
color = np.tile(np.arange(count.shape[0]),
(count.shape[1], 1)).T
fig, ax = plt.subplots(figsize=(12, 6))
ax.scatter(x, count + 0.1, lw=2, c=color)
ax.set_xlabel('Position [bp]')
ax.set_ylabel('Coverage')
ax.set_xlim(-1, count.shape[-1])
ax.set_ylim(ymin=0.09)
ax.set_yscale('log')
ax.grid(True)
if VERBOSE >= 1:
print samplename
sample = SamplePat(sample)
pname = sample.patient
conss_genomewide = SeqIO.read(
get_initial_reference_filename(pname, 'genomewide'), 'fasta')
# Collect the allele counts (where possible)
acs = []
for fragment in ['F' + str(i) for i in xrange(1, 7)]:
try:
ref = ''.join(
SeqIO.read(get_initial_reference_filename(pname, fragment),
'fasta'))
ac = sample.get_allele_counts(fragment, merge_read_types=False)
acs.append((fragment, ref, ac))
except IOError:
continue
if not len(acs):
if VERBOSE >= 1:
print 'No data found: skipping'
continue
# Merge allele counts
ac = merge_allele_counts(conss_genomewide, acs, VERBOSE=VERBOSE)
if save_to_file:
fn_out = sample.get_allele_counts_filename('genomewide')
np.save(fn_out, ac)
if VERBOSE >= 1:
if pnames is not None:
samples = samples.loc[samples.patient.isin(pnames)]
elif samplenames is not None:
samples = samples.loc[samples.index.isin(samplenames)]
if VERBOSE >= 2:
print 'samples', samples.index.tolist()
for region in regions:
for samplename, sample in samples.iterrows():
sample = SamplePat(sample)
if VERBOSE >= 1:
print region, samplename
count = sample.get_allele_counts(region, qual_min=qual_min)
if use_plot:
x = np.tile(np.arange(count.shape[1]), (count.shape[0], 1))
color = np.tile(np.arange(count.shape[0]), (count.shape[1], 1)).T
fig, ax = plt.subplots(figsize=(12, 6))
ax.scatter(x, count + 0.1, lw=2, c=color)
ax.set_xlabel('Position [bp]')
ax.set_ylabel('Coverage')
ax.set_xlim(-1, count.shape[-1])
ax.set_ylim(ymin=0.09)
ax.set_yscale('log')
ax.grid(True)
ax.set_title(samplename+', '+region)
samples = samples.loc[samples.patient.isin(pnames)]
elif samplenames is not None:
samples = samples.loc[samples.index.isin(samplenames)]
if VERBOSE >= 2:
print 'samples', samples.index.tolist()
data = defaultdict(dict)
for samplename, sample in samples.iterrows():
sample = SamplePat(sample)
if VERBOSE >= 1:
print samplename
for (fr1, fr2) in izip(fragments[:-1], fragments[1:]):
try:
ac1 = sample.get_allele_counts(fr1)
ac2 = sample.get_allele_counts(fr2)
except IOError:
continue
if VERBOSE >= 2:
print fr1, fr2
# Filter positions by coverage
covmin = 100
indcm1 = (ac1.sum(axis=0) >= covmin)
indcm2 = (ac2.sum(axis=0) >= covmin)
ac1 = ac1[:, indcm1]
ac2 = ac2[:, indcm2]
c1 = alpha[ac1.argmax(axis=0)]
print 'samples', samples.index.tolist()
for samplename, sample in samples.iterrows():
if VERBOSE >= 1:
print samplename
sample = SamplePat(sample)
pname = sample.patient
conss_genomewide = SeqIO.read(get_initial_reference_filename(pname, 'genomewide'), 'fasta')
# Collect the allele counts (where possible)
acs = []
for fragment in ['F'+str(i) for i in xrange(1, 7)]:
try:
ref = ''.join(SeqIO.read(get_initial_reference_filename(pname, fragment), 'fasta'))
ac = sample.get_allele_counts(fragment, merge_read_types=False)
acs.append((fragment, ref, ac))
except IOError:
continue
if not len(acs):
if VERBOSE >= 1:
print 'No data found: skipping'
continue
# Merge allele counts
ac = merge_allele_counts(conss_genomewide, acs, VERBOSE=VERBOSE)
if save_to_file:
fn_out = sample.get_allele_counts_filename('genomewide')
np.save(fn_out, ac)
if VERBOSE >= 1: