VERBOSE=VERBOSE,
qual_min=qual_min)
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
if submit:
fork_self(samplename, protein, VERBOSE=VERBOSE, qual_min=qual_min)
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
