def read_tabix(file_name,
genotyped_id_file=os.environ['OBER_DATA'] +
'/hutt/hutt.3chipoverlap.clean.fam'):
'''Read a Haplotype object from an ITABIX CGI-imputed file.
Line format: tab-delimited
7849538 chr11 1909005 1909006 snp T C dbsnp.107:rs3817198 <genotypes>
'''
# Load entire file into memory. It must fit, if we are to load it into a Genotype object
d = np.loadtxt(file_name, str)
# Read SNP metadata into a record array
snp_dtype = [
('chrom', np.uint8), # Chromosome # containing the SNP
('name', np.chararray), # SNP name (e.g., 'rs...')
('dist_cm', np.float), # Genetic position [CENTI-Morgans!!]
('base_pair', np.uint) # Base pair position on chromosome
]
snp = np.array([(int(line[1][3:]), line[7], 0, int(line[3]))
for line in d],
dtype=snp_dtype)
data = np.array([[(CGI_LETTER_TO_ALLELE[x[1]], CGI_LETTER_TO_ALLELE[x[2]])
for x in line[8:]] for line in d])
hap_type = np.array([[int(x[0]) for x in line[8:]] for line in d])
sample_id = read_sample_id(genotyped_id_file)
# Construct object
return GenotypeFactory.new_instance('haplotype',
data,
snp,
sample_id,
hap_type=hap_type)
def __init__(self, file_name, affy_bim, genotyped_id_file, debug=False):
p = im.hutt_pedigree()
self.qf = p.quasi_founders
self.non_qf = np.setdiff1d(xrange(p.num_genotyped), p.quasi_founders)
self.debug = debug
# Load affy SNP names
self.affy = set(np.loadtxt(affy_bim, usecols=[1], dtype=str))
self.sample_id = read_sample_id(genotyped_id_file)
# Load data, cache statistics in the data field
self.data = self.__stats_struct(file_name)
def __init__(self, file_name, affy_bim, genotyped_id_file, debug=False):
p = im.hutt_pedigree()
self.qf = p.quasi_founders
self.non_qf = np.setdiff1d(xrange(p.num_genotyped), p.quasi_founders)
self.debug = debug
# Load affy SNP names
self.affy = set(np.loadtxt(affy_bim, usecols=[1], dtype=str))
self.sample_id = read_sample_id(genotyped_id_file)
# Load data, cache statistics in the data field
self.data = self.__stats_struct(file_name)
def read_tabix(file_name, genotyped_id_file=os.environ["OBER_DATA"] + "/hutt/hutt.3chipoverlap.clean.fam"):
"""Read a Haplotype object from an ITABIX CGI-imputed file.
Line format: tab-delimited
7849538 chr11 1909005 1909006 snp T C dbsnp.107:rs3817198 <genotypes>
"""
# Load entire file into memory. It must fit, if we are to load it into a Genotype object
d = np.loadtxt(file_name, str)
# Read SNP metadata into a record array
snp_dtype = [
("chrom", np.uint8), # Chromosome # containing the SNP
("name", np.chararray), # SNP name (e.g., 'rs...')
("dist_cm", np.float), # Genetic position [CENTI-Morgans!!]
("base_pair", np.uint), # Base pair position on chromosome
]
snp = np.array([(int(line[1][3:]), line[7], 0, int(line[3])) for line in d], dtype=snp_dtype)
data = np.array([[(CGI_LETTER_TO_ALLELE[x[1]], CGI_LETTER_TO_ALLELE[x[2]]) for x in line[8:]] for line in d])
hap_type = np.array([[int(x[0]) for x in line[8:]] for line in d])
sample_id = read_sample_id(genotyped_id_file)
# Construct object
return GenotypeFactory.new_instance("haplotype", data, snp, sample_id, hap_type=hap_type)