patient = Patient(patient)
# Make maps for all annotations if not explicit
if regions is None:
patseqann = patient.get_reference('genomewide', format='gb')
regionspat = map(attrgetter('id'), patseqann.features) + ['genomewide']
else:
regionspat = regions
for region in regionspat:
if VERBOSE >= 1:
print pname, region
refseq = load_custom_reference(refname, format='gb', region=region)
patseq = patient.get_reference(region)
mapco = build_coordinate_map(refseq, patseq, VERBOSE=VERBOSE)
mapco = np.array(mapco, int)
shift_mapco(mapco, refname, region)
maps_coord[(region, pname)] = mapco
if save_to_file:
out_fn = get_coordinate_map_filename(pname, region, refname=refname)
np.savetxt(out_fn, mapco, fmt='%d',
delimiter='\t',
header=refname+'\t'+pname+'_'+region)
if VERBOSE:
print 'Saved to file:', pname, region
def get_map_coordinates_reference_filename(self, fragment, refname='HXB2'):
'''Get the filename of the coordinate map to an external reference'''
from hivwholeseq.patients.filenames import get_coordinate_map_filename
return get_coordinate_map_filename(self.name,
fragment,
refname=refname)
def get_map_coordinates_reference_filename(self, fragment, refname='HXB2'):
'''Get the filename of the coordinate map to an external reference'''
from hivwholeseq.patients.filenames import get_coordinate_map_filename
return get_coordinate_map_filename(self.name, fragment, refname=refname)
patseqann = patient.get_reference('genomewide', format='gb')
regionspat = map(attrgetter('id'),
patseqann.features) + ['genomewide']
else:
regionspat = regions
for region in regionspat:
if VERBOSE >= 1:
print pname, region
refseq = load_custom_reference(refname, format='gb', region=region)
patseq = patient.get_reference(region)
mapco = build_coordinate_map(refseq, patseq, VERBOSE=VERBOSE)
mapco = np.array(mapco, int)
shift_mapco(mapco, refname, region)
maps_coord[(region, pname)] = mapco
if save_to_file:
out_fn = get_coordinate_map_filename(pname,
region,
refname=refname)
np.savetxt(out_fn,
mapco,
fmt='%d',
delimiter='\t',
header=refname + '\t' + pname + '_' + region)
if VERBOSE:
print 'Saved to file:', pname, region
if pnames is None:
patients = [p for p in patients_all]
else:
patients = [p for p in patients_all if p.id in pnames]
if not len(patients):
raise ValueError('No patients found!')
if VERBOSE >= 3:
print 'patients', map(attrgetter('id'), patients)
for patient in patients:
pname = patient.id
found = False
for fragment in ['F'+str(i+1) for i in xrange(7)] + ['genomewide']:
map_fn = get_coordinate_map_filename(pname, fragment, refname=refname)
mapco = np.loadtxt(map_fn, dtype=int, unpack=True)
frag_start = mapco[0, 0]
frag_end = mapco[0, -1] + 1
if (frag_start <= coords[0]) and (frag_end + 1 >= coords[1]):
found = True
break
if not found:
raise ValueError('Window not found in any fragment or genomewide')
if coords[0] in mapco[0]:
win_start_init = mapco[1, mapco[0] == coords[0]][0]
else:
found = False