def main():
arg_ct = len(sys.argv)
if arg_ct < 4:
print "Usage: python hamming_distance.py [.bed/.pgen] [sample index 1] [sample index 2] {raw_sample_ct=[val]}"
print "* raw_sample_ct is required for .bed files."
return
specified_sample_ct = None
sample_ct = 2
sample_subset = np.empty(sample_ct, np.uint32)
sample_subset[0] = int(sys.argv[2])
sample_subset[1] = int(sys.argv[3])
if arg_ct > 4:
if not sys.argv[4].startswith("raw_sample_ct="):
print "Error: Invalid raw_sample_ct parameter."
return
specified_sample_ct = int(sys.argv[4][14:])
with pgenlib.PgenReader(sys.argv[1],
raw_sample_ct=specified_sample_ct,
sample_subset=sample_subset) as pf:
variant_ct = pf.get_variant_ct()
hamming_distance = 0
buf = np.empty(sample_ct, np.int8)
for vidx in xrange(variant_ct):
pf.read(vidx, buf)
geno0 = buf[0]
geno1 = buf[1]
if geno0 != -9 and geno1 != -9:
hamming_distance += abs(geno0 - geno1)
sys.stdout.write("Hamming distance: " + str(hamming_distance))
sys.stdout.write('\n')
def main():
arg_ct = len(sys.argv)
if arg_ct < 3:
print(
"Usage: python3 pgen_subset_and_compress.py <input .bed/.pgen> <output .pgen name> [raw_sample_ct=<val>] [sample idx(s)...]"
)
print("* raw_sample_ct is required for .bed files.")
print("* sample indexes must be in increasing order.")
print("* This currently assumes that A2 alleles are always reference.")
return
sample_subset = None
specified_sample_ct = None
sample_ct = None
if arg_ct > 3:
offset = 3
if sys.argv[3].startswith("raw_sample_ct="):
specified_sample_ct = int(sys.argv[3][14:])
offset = 4
if arg_ct > offset:
sample_ct = arg_ct - offset
sample_subset = np.empty(sample_ct, np.uint32)
for idx in range(sample_ct):
sample_subset[idx] = int(sys.argv[offset + idx])
with pgenlib.PgenReader(bytes(sys.argv[1], 'utf8'),
raw_sample_ct=specified_sample_ct,
sample_subset=sample_subset) as infile:
raw_sample_ct = infile.get_raw_sample_ct()
if sample_ct is None:
sample_ct = raw_sample_ct
variant_ct = infile.get_variant_ct()
hardcall_phase_present = infile.hardcall_phase_present()
geno_buf = None
allele_code_buf = None
phasepresent_buf = None
if not hardcall_phase_present:
geno_buf = np.empty(sample_ct, np.int8)
else:
allele_code_buf = np.empty(sample_ct * 2, np.int32)
phasepresent_buf = np.empty(sample_ct, np.bool_)
with pgenlib.PgenWriter(
bytes(sys.argv[2], 'utf8'),
sample_ct,
variant_ct,
False,
hardcall_phase_present=hardcall_phase_present) as outfile:
if not hardcall_phase_present:
for vidx in range(variant_ct):
infile.read(vidx, geno_buf)
outfile.append_biallelic(geno_buf)
else:
for vidx in range(variant_ct):
infile.read_alleles_and_phasepresent(
vidx, allele_code_buf, phasepresent_buf)
outfile.append_partially_phased(allele_code_buf,
phasepresent_buf)
return
def read_alleles_block(pgen_f, bins_df, block_id):
"""wrapper function of pgenlib.PgenReader.read_alleles_range for a LD block"""
bim_s = bins_df.bimIdStart[block_id]
bim_e = bins_df.bimIdEnd[block_id]
with pg.PgenReader(pgen_f) as pgr:
buf_ndary = np.zeros((bim_e - bim_s, pgr.get_raw_sample_ct() * 2),
dtype=np.int32)
pgr.read_alleles_range(bim_s, bim_e, buf_ndary)
return buf_ndary
def main():
arg_ct = len(sys.argv)
if arg_ct < 3:
print(
"Usage: python single_variant_test.py <.bed/.pgen> <variant idx> [raw_sample_ct=<val>] [sample idx(s)...]"
)
print("* raw_sample_ct is required for .bed files.")
print("* sample indexes must be in increasing order.")
return
sample_subset = None
specified_sample_ct = None
sample_ct = None
if arg_ct > 3:
offset = 3
if sys.argv[3].startswith("raw_sample_ct="):
specified_sample_ct = int(sys.argv[3][14:])
offset = 4
if arg_ct > offset:
sample_ct = arg_ct - offset
sample_subset = np.empty(sample_ct, np.uint32)
for idx in range(sample_ct):
sample_subset[idx] = int(sys.argv[offset + idx])
vidx = int(sys.argv[2])
with pgenlib.PgenReader(bytes(sys.argv[1], 'utf8'),
raw_sample_ct=specified_sample_ct,
sample_subset=sample_subset) as pf:
raw_sample_ct = pf.get_raw_sample_ct()
if sample_ct is None:
sample_ct = raw_sample_ct
# variant_ct = pf.get_variant_ct()
buf = np.empty(raw_sample_ct * 2, np.int32)
buf2 = np.empty(raw_sample_ct, np.bool_)
pf.read_alleles_and_phasepresent(vidx, buf, buf2)
for sample_idx in range(sample_ct):
sys.stdout.write(str(buf[2 * sample_idx]))
if buf2[sample_idx]:
sys.stdout.write('|')
else:
sys.stdout.write('/')
sys.stdout.write(str(buf[2 * sample_idx + 1]))
sys.stdout.write(' ')
sys.stdout.write('\n')
pf.change_sample_subset()
pf.read_alleles_and_phasepresent(vidx, buf, buf2)
for sample_idx in range(raw_sample_ct):
sys.stdout.write(str(buf[2 * sample_idx]))
if buf2[sample_idx]:
sys.stdout.write('|')
else:
sys.stdout.write('/')
sys.stdout.write(str(buf[2 * sample_idx + 1]))
sys.stdout.write(' ')
sys.stdout.write('\n')
def main():
arg_ct = len(sys.argv)
if arg_ct < 2:
print(
"Usage: python3 het_count.py <.bed/.pgen> [raw_sample_ct=<val>] [sample idx(s)...]"
)
print("* raw_sample_ct is required for .bed files.")
print("* sample indexes must be in increasing order.")
print(
"* The Python side of this is really slow if you don't explicitly specify sample indexes."
)
return
sample_subset = None
specified_sample_ct = None
sample_ct = None
if arg_ct > 2:
offset = 2
if sys.argv[2].startswith("raw_sample_ct="):
specified_sample_ct = int(sys.argv[2][14:])
offset = 3
if arg_ct > offset:
sample_ct = arg_ct - offset
sample_subset = np.empty(sample_ct, np.uint32)
for idx in range(sample_ct):
sample_subset[idx] = int(sys.argv[offset + idx])
with pgenlib.PgenReader(bytes(sys.argv[1], 'utf8'),
raw_sample_ct=specified_sample_ct,
sample_subset=sample_subset) as pf:
raw_sample_ct = pf.get_raw_sample_ct()
if sample_ct is None:
sample_ct = raw_sample_ct
variant_ct = pf.get_variant_ct()
tot_hets = np.zeros((sample_ct, ), dtype=np.uint32)
buf = np.empty(sample_ct, np.int8)
for vidx in range(variant_ct):
pf.read(vidx, buf)
# this is horribly inefficient...
for sample_idx in range(sample_ct):
if buf[sample_idx] == 1:
tot_hets[sample_idx] += 1
for sample_idx in range(sample_ct):
sys.stdout.write(str(tot_hets[sample_idx]))
sys.stdout.write(' ')
sys.stdout.write('\n')
def main():
arg_ct = len(sys.argv)
if arg_ct < 3:
print(
"Usage: python3 extract_haps.py <.bed/.pgen> <output filename> [raw_sample_ct=<val>] [sample idx(s)...]"
)
print("* raw_sample_ct is required for .bed files.")
return
sample_subset = None
specified_sample_ct = None
sample_ct = None
if arg_ct > 3:
offset = 3
if sys.argv[3].startswith("raw_sample_ct="):
specified_sample_ct = int(sys.argv[3][14:])
if arg_ct > offset:
sample_ct = arg_ct - offset
sample_subset = np.empty(sample_ct, np.uint32)
for idx in range(sample_ct):
sample_subset[idx] = int(sys.argv[offset + idx])
with pgenlib.PgenReader(bytes(sys.argv[1], 'utf8'),
raw_sample_ct=specified_sample_ct,
sample_subset=sample_subset) as infile:
raw_sample_ct = infile.get_raw_sample_ct()
if sample_ct is None:
sample_ct = raw_sample_ct
variant_ct = infile.get_variant_ct()
allele_code_buf = np.empty([sample_ct * 2, variant_ct], dtype=np.int32)
infile.read_alleles_range(0, variant_ct, allele_code_buf, 1)
with open(sys.argv[2], 'w') as outfile:
for vidx in range(variant_ct):
for sidx in range(sample_ct):
if sidx != 0:
outfile.write(' ')
outfile.write(
str(allele_code_buf[2 * sidx, vidx]) + "|" +
str(allele_code_buf[2 * sidx + 1, vidx]))
outfile.write('\n')
vec_rr = 1.0 / np.sqrt(vec_rr)
mat_covar = np.transpose(np.transpose(mat_covar) * vec_rr)
# qr decomposition of covariate matrix
Q = linalg.qr(mat_covar, mode="economic")[0]
del mat_covar
print("Completed QR decomposition of covariate matrix.")
'''
Read .pvar file.
Read pgen/bed file and do single-variant assoc tests.
Write stats to output file on the fly.
'''
print("Starting assoc tests...")
print("Writing stats into", args.out)
outfp = open(args.out, "w")
pf = pgenlib.PgenReader(pgen.encode(),
raw_sample_ct=raw_sample_ct,
sample_subset=sample_subset)
with open(pvar) as fp:
var_idx = -1
int8vec_x = np.empty(sample_ct, dtype=np.int8)
vec_x = np.empty(sample_ct, dtype=np.float32)
for line in fp:
if line[0] == '#':
continue
if line.strip() is not None:
var_idx += 1
if var_idx > args.end:
break
if var_idx % 1000 == 0:
print(" Scanning variant", var_idx)
if var_idx >= args.begin:
def load(self, chromosome):
self.pgen[self.uniq_key(chromosome)] = \
pg.PgenReader(self.filename)
