def get_region(c, args):
region_regex = re.compile("(\S+):(\d+)-(\d+)")
try:
region = region_regex.findall(args.region)[0]
except IndexError:
sys.exit("Malformed region (--reg) string")
if len(region) != 3:
sys.exit("Malformed region (--reg) string")
chrom = region[0]
start = region[1]
end = region[2]
query = "SELECT * \
FROM variants v \
WHERE v.chrom = " + "'" + chrom + "'" + \
" AND ((v.start BETWEEN " + start + " AND " + end + ")" +\
" OR (v.end BETWEEN " + start + " AND " + end + "))" + \
"ORDER BY chrom, start"
c.execute(query)
# build a list of all the column indices that are NOT
# gt_* columns. These will be the columns reported
(col_names, non_gt_idxs) = \
util.get_col_names_and_indices(c.description, ignore_gt_cols=True)
if args.use_header:
print args.separator.join(col for col in col_names)
for row in c:
print args.separator.join(str(row[i]) if row[i] is not None else "."
for i in non_gt_idxs)
def get_genotypes(conn, metadata, args):
"""For each variant, report each sample's genotype
on a separate line.
"""
idx_to_sample = util.map_indices_to_samples(metadata)
query = "SELECT v.chrom, v.start, v.end, \
v.ref, v.alt, \
v.type, v.sub_type, \
v.aaf, v.in_dbsnp, v.gene, \
v.gts \
FROM variants v \
ORDER BY chrom, start"
res = conn.execute(sql.text(query))
# build a list of all the column indices that are NOT
# gt_* columns. These will be the columns reported
(col_names, non_gt_idxs) = \
util.get_col_names_and_indices(metadata.tables["variants"], ignore_gt_cols=True)
col_names.append('sample')
col_names.append('genotype')
if args.use_header:
print args.separator.join(col for col in col_names)
for row in res:
gts = Z.unpack_genotype_blob(row['gts'])
for idx, gt in enumerate(gts):
# xrange(len(row)-1) to avoid printing v.gts
a = args.separator.join(str(row[i]) for i in xrange(len(row)-1))
b = args.separator.join([idx_to_sample[idx], gt])
print args.separator.join((a, b))
def get_genotypes(c, args):
"""For each variant, report each sample's genotype
on a separate line.
"""
idx_to_sample = util.map_indicies_to_samples(c)
query = "SELECT v.chrom, v.start, v.end, \
v.ref, v.alt, \
v.type, v.sub_type, \
v.aaf, v.in_dbsnp, v.gene, \
v.gts \
FROM variants v \
ORDER BY chrom, start"
c.execute(query)
# build a list of all the column indices that are NOT
# gt_* columns. These will be the columns reported
(col_names, non_gt_idxs) = \
util.get_col_names_and_indices(c.description, ignore_gt_cols=True)
col_names.append('sample')
col_names.append('genotype')
if args.use_header:
print args.separator.join(col for col in col_names)
for row in c:
gts = np.array(cPickle.loads(zlib.decompress(row['gts'])))
for idx, gt in enumerate(gts):
# xrange(len(row)-1) to avoid printing v.gts
print args.separator.join(
str(row[i]) for i in xrange(len(row) - 1)),
print args.separator.join([idx_to_sample[idx], gt])
def get_genotypes(c, args):
"""For each variant, report each sample's genotype
on a separate line.
"""
idx_to_sample = util.map_indices_to_samples(c)
query = "SELECT v.chrom, v.start, v.end, \
v.ref, v.alt, \
v.type, v.sub_type, \
v.aaf, v.in_dbsnp, v.gene, \
v.gts \
FROM variants v \
ORDER BY chrom, start"
c.execute(query)
# build a list of all the column indices that are NOT
# gt_* columns. These will be the columns reported
(col_names, non_gt_idxs) = \
util.get_col_names_and_indices(c.description, ignore_gt_cols=True)
col_names.append('sample')
col_names.append('genotype')
if args.use_header:
print args.separator.join(col for col in col_names)
for row in c:
gts = np.array(cPickle.loads(zlib.decompress(row['gts'])))
for idx, gt in enumerate(gts):
# xrange(len(row)-1) to avoid printing v.gts
print args.separator.join(str(row[i]) for i in xrange(len(row)-1)),
print args.separator.join([idx_to_sample[idx], gt])
def get_samples(c, args):
"""
Report all of the information about the samples in the DB
"""
query = "SELECT * FROM samples"
c.execute(query)
(col_names, col_idxs) = util.get_col_names_and_indices(c.description)
if args.use_header:
print args.separator.join(col_names)
for row in c:
print args.separator.join(str(row[i]) if row[i] is not None else "." \
for i in xrange(len(row)) )
def get_samples(c, args):
"""
Report all of the information about the samples in the DB
"""
query = "SELECT * FROM samples"
c.execute(query)
(col_names, col_idxs) = util.get_col_names_and_indices(c.description)
if args.use_header:
print args.separator.join(col_names)
for row in c:
print args.separator.join(str(row[i]) if row[i] is not None else "." \
for i in xrange(len(row)) )
def get_samples(conn, metadata, args):
"""
Report all of the information about the samples in the DB
"""
query = "SELECT * FROM samples"
res = conn.execute(query)
(col_names, col_idxs) = util.get_col_names_and_indices(metadata.tables["samples"])
if args.use_header:
print args.separator.join(col_names)
for row in res:
print args.separator.join(str(row[i]) if row[i] is not None else "." \
for i in xrange(len(row)) )
def get_samples(conn, metadata, args):
"""
Report all of the information about the samples in the DB
"""
query = "SELECT * FROM samples"
res = conn.execute(query)
(col_names, col_idxs) = util.get_col_names_and_indices(metadata.tables["samples"])
if args.use_header:
print args.separator.join(col_names)
for row in res:
print args.separator.join(str(row[i]) if row[i] is not None else "." \
for i in xrange(len(row)) )
def get_variants(conn, metadata, args):
"""
Report all columns in the variant table, except for the
genotype vectors.
"""
query = "SELECT * FROM variants \
ORDER BY chrom, start"
res = conn.execute(query)
# build a list of all the column indices that are NOT
# gt_* columns. These will be the columns reported
(col_names, non_gt_idxs) = \
util.get_col_names_and_indices(metadata.tables["variants"], ignore_gt_cols=True)
if args.use_header:
print args.separator.join(col for col in col_names)
for row in res:
print args.separator.join('.' if (row[i] is None) else row[i].encode('utf-8') if type(row[i]) is unicode else str(row[i]) for i in non_gt_idxs)
def get_variants(conn, metadata, args):
"""
Report all columns in the variant table, except for the
genotype vectors.
"""
query = "SELECT * FROM variants \
ORDER BY chrom, start"
res = conn.execute(query)
# build a list of all the column indices that are NOT
# gt_* columns. These will be the columns reported
(col_names, non_gt_idxs) = \
util.get_col_names_and_indices(metadata.tables["variants"], ignore_gt_cols=True)
if args.use_header:
print args.separator.join(col for col in col_names)
for row in res:
print args.separator.join('.' if (row[i] is None) else row[i].encode('utf-8') if type(row[i]) is unicode else str(row[i]) for i in non_gt_idxs)
def get_variants(c, args):
"""
Report all columns in the variant table, except for the
genotype vectors.
"""
query = "SELECT * FROM variants \
ORDER BY chrom, start"
c.execute(query)
# build a list of all the column indices that are NOT
# gt_* columns. These will be the columns reported
(col_names, non_gt_idxs) = \
util.get_col_names_and_indices(c.description, ignore_gt_cols=True)
if args.use_header:
print args.separator.join(col for col in col_names)
for row in c:
print args.separator.join(str(row[i]) if row[i] is not None else "." \
for i in non_gt_idxs )
def get_variants(c, args):
"""
Report all columns in the variant table, except for the
genotype vectors.
"""
query = "SELECT * FROM variants \
ORDER BY chrom, start"
c.execute(query)
# build a list of all the column indices that are NOT
# gt_* columns. These will be the columns reported
(col_names, non_gt_idxs) = \
util.get_col_names_and_indices(c.description, ignore_gt_cols=True)
if args.use_header:
print args.separator.join(col for col in col_names)
for row in c:
print args.separator.join(str(row[i]) if row[i] is not None else "." \
for i in non_gt_idxs )
def get_genotypes(conn, metadata, args):
"""For each variant, report each sample's genotype
on a separate line.
"""
idx_to_sample = util.map_indices_to_samples(metadata)
query = "SELECT v.chrom, v.start, v.end, \
v.ref, v.alt, \
v.type, v.sub_type, \
v.aaf, v.in_dbsnp, v.gene, \
v.gts \
FROM variants v \
ORDER BY chrom, start"
res = conn.execute(sql.text(query))
# build a list of all the column indices that are NOT
# gt_* columns. These will be the columns reported
(col_names, non_gt_idxs) = \
util.get_col_names_and_indices(metadata.tables["variants"], ignore_gt_cols=True)
col_names.append('sample')
col_names.append('genotype')
if args.use_header:
print args.separator.join(col for col in col_names)
unpack = Z.unpack_genotype_blob
import zlib
for row in res:
try:
gts = unpack(row['gts'])
except zlib.error:
unpack = Z.snappy_unpack_blob
gts = unpack(row['gts'])
for idx, gt in enumerate(gts):
# xrange(len(row)-1) to avoid printing v.gts
a = args.separator.join(str(row[i]) for i in xrange(len(row)-1))
b = args.separator.join([idx_to_sample[idx], gt])
print args.separator.join((a, b))
def get_gene(c, args):
"""
Report all variants in a specific gene.
"""
query = "SELECT * \
FROM variants v \
WHERE v.gene = " + "'" + args.gene + "' " \
"ORDER BY chrom, start"
c.execute(query)
# build a list of all the column indices that are NOT
# gt_* columns. These will be the columns reported
(col_names, non_gt_idxs) = \
util.get_col_names_and_indices(c.description, ignore_gt_cols=True)
if args.use_header:
print args.separator.join(col for col in col_names)
for row in c:
print args.separator.join(str(row[i]) if row[i] is not None else "."
for i in non_gt_idxs)
