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 protein in proteins:
for samplename, sample in samples.iterrows():
sample = SamplePat(sample)
if VERBOSE >= 1:
print protein, samplename
count = sample.get_allele_counts_aa(protein, 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 [aa]')
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 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 protein in proteins:
for samplename, sample in samples.iterrows():
sample = SamplePat(sample)
if VERBOSE >= 1:
print protein, samplename
count = sample.get_allele_counts_aa(protein, 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 [aa]')
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+', '+protein)
