if VERBOSE >= 1:
print protein, samplename
sample = SamplePat(sample)
# NOTE: How do we find what fragment covers the protein? Well, a
# protein can happily cross fragments. Since each
# codon is independent, we should iterate over codons. We do not
# do that for efficiency reasons. Instead, we identify all potential
# fragments and split the protein into full codon chunks covered by
# a single fragment.
fragment_rois = sample.get_fragments_covered(
protein, include_coordinates=True)
refseq = sample.get_reference(protein)
fn_out = sample.get_allele_counts_filename(protein,
PCR=PCR,
qual_min=qual_min,
type='aa')
from hivwholeseq.utils.sequence import alphaa
count = np.zeros((len(alphaa), len(refseq) // 3), int)
for frroi in fragment_rois:
fragment = frroi['name']
start_fr, end_fr = frroi['fragment']
start, end = frroi['roi']
# Check that we align with codons
rf = start % 3
if rf:
samples = lssp()
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 samplename, sample in samples.iterrows():
if VERBOSE >= 1:
print samplename
sample = SamplePat(sample)
pname = sample.patient
ref = sample.get_reference('genomewide', 'gb')
# Collect the insertions (where possible)
ics = {}
for fragment in ['F' + str(i) for i in xrange(1, 7)]:
try:
ic = sample.get_insertions(fragment, merge_read_types=False)
except IOError:
continue
start = find_annotation(ref, fragment).location.nofuzzy_start
ics[(fragment, start)] = ic
if not len(ics):
if VERBOSE >= 1:
print 'No data found: skipping'
continue
samples = lssp()
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 samplename, sample in samples.iterrows():
if VERBOSE >= 1:
print samplename
sample = SamplePat(sample)
pname = sample.patient
ref = sample.get_reference("genomewide", "gb")
# Collect the insertions (where possible)
ics = {}
for fragment in ["F" + str(i) for i in xrange(1, 7)]:
try:
ic = sample.get_insertions(fragment, merge_read_types=False)
except IOError:
continue
start = find_annotation(ref, fragment).location.nofuzzy_start
ics[(fragment, start)] = ic
if not len(ics):
if VERBOSE >= 1:
print "No data found: skipping"
continue
if VERBOSE >= 1:
print protein, samplename
sample = SamplePat(sample)
# NOTE: How do we find what fragment covers the protein? Well, a
# protein can happily cross fragments. Since each
# codon is independent, we should iterate over codons. We do not
# do that for efficiency reasons. Instead, we identify all potential
# fragments and split the protein into full codon chunks covered by
# a single fragment.
fragment_rois = sample.get_fragments_covered(protein,
include_coordinates=True)
refseq = sample.get_reference(protein)
fn_out = sample.get_allele_counts_filename(protein, PCR=PCR,
qual_min=qual_min,
type='aa')
from hivwholeseq.utils.sequence import alphaa
count = np.zeros((len(alphaa), len(refseq) // 3), int)
for frroi in fragment_rois:
fragment = frroi['name']
start_fr, end_fr = frroi['fragment']
start, end = frroi['roi']
# Check that we align with codons
rf = start % 3
if rf:
start_fr += 3 - rf
