def haplotypes(self, fragment, start, stop, VERBOSE=0, maxreads=-1, filters=None):
from hivwholeseq.patients.get_local_haplotypes import get_local_haplotypes
from .filenames import get_mapped_filtered_filename
bam_fname = get_mapped_filtered_filename(self.patient, self.name, fragment, type='bam', decontaminated=True)
try:
return get_local_haplotypes(bam_fname, start, stop)
except:
raise ValueError("can't read haplotypes")
def haplotypes(self, fragment, start, stop, VERBOSE=0, maxreads=-1, filters=None):
from hivwholeseq.patients.get_local_haplotypes import get_local_haplotypes
from .filenames import get_mapped_filtered_filename
bam_fname = get_mapped_filtered_filename(self.patient, self.name, fragment, type='bam', decontaminated=True)
try:
return get_local_haplotypes(bam_fname, start, stop)
except:
raise ValueError("can't read haplotypes")
def get_local_haplotypes(self,
fragment,
start,
end,
VERBOSE=0,
maxreads=-1,
filters=None,
PCR=1):
'''Get local haplotypes'''
from hivwholeseq.patients.get_local_haplotypes import get_local_haplotypes
bamfilename = self.get_mapped_filtered_filename(fragment, PCR=PCR)
haplo = get_local_haplotypes(bamfilename,
start,
end,
VERBOSE=VERBOSE,
maxreads=maxreads,
label=self.name)
if filters is not None:
if 'noN' in filters:
hnames = [hname for hname in haplo.iterkeys() if 'N' in hname]
for hname in hnames:
del haplo[hname]
if 'nosingletons' in filters:
hnames = [hname for hname, c in haplo.iteritems() if c <= 1]
for hname in hnames:
del haplo[hname]
if any('mincount=' in ft for ft in filters):
for ft in filters:
if 'mincount=' in ft:
break
cmin = int(ft[len('mincount='):])
hnames = [hname for hname, c in haplo.iteritems() if c < cmin]
for hname in hnames:
del haplo[hname]
if any('freqmin=' in ft for ft in filters):
for ft in filters:
if 'freqmin=' in ft:
break
fmin = float(ft[len('minfreq='):])
csum = sum(haplo.itervalues())
hnames = [
hname for hname, c in haplo.iteritems() if c < fmin * csum
]
for hname in hnames:
del haplo[hname]
return haplo
