def read_plink(**kwargs):
'''Load a problem from the following PLINK files:
Default Override Option Data Format
======================================================================================
prefix.pdg.tfam pedigree Pedigree adjacency PLINK TFAM
(genotyped+nongenotyped samples)
prefix.tfam pedigree_genotyped Genotyped sample pedigree
(sub-graph of the pedigree) PLINK TFAM
corresponding to prefix.tped
prefix.tped genotype Genotype data PLINK TPED
prefix.hap.tped haplotype* Haplotype data PLINK TPED
prefix.err error** Genotype errors flagged Integer array (snps x samples)
prefix.info info Problem info pickle (binary)
prefix.frm frames LD-independent SNP frames text file
prefix.lam lam*** Haplotype est. recombination rate text file
* - hap data not loaded if this option is None.
** - errors set to 0 if this file is not found or this option is set to None.
*** - data not loaded if if this file is not found.
'''
# Read input options
verbose = kwargs.get('verbose', False)
prefix = kwargs.get('prefix', '')
overrideable_option = lambda name, default: kwargs.get(name, default if prefix else None)
pedigree = overrideable_option('pedigree', prefix + '.pdg.tfam')
pedigree_genotyped = overrideable_option('pedigree_genotyped', prefix + '.tfam')
genotype = overrideable_option('genotype', prefix + '.tped')
haplotype = overrideable_option('haplotype', prefix + '.hap.tped')
error_file = overrideable_option('error', prefix + '.err')
info = overrideable_option('info', prefix + '.info')
if not np.all([[pedigree, pedigree_genotyped, genotype, error_file] is not None]):
raise ValueError('Must specify a prefix or pedigree, pedigree_genotyped, genotype, error files')
frames_file = overrideable_option('frames', prefix + '.frm')
lam_file = overrideable_option('lam', prefix + '.lam')
# Load data
print_location = lambda x : x if x else '-'
if verbose: print 'Reading pedigree from %s, %s ...' % (print_location(pedigree), print_location(pedigree_genotyped),)
p = io_pedigree.read(pedigree, genotyped_id_file=pedigree_genotyped)
if verbose: print 'Reading genotype data from %s ...' % (print_location(genotype),)
g = io_genotype.read('plink', 'genotype', tped=genotype, load_ids=False)
if verbose: print 'Reading haplotype data from %s ...' % (print_location(haplotype),)
h = io_genotype.read('plink', 'haplotype', tped=haplotype, load_ids=False) if haplotype else None
if verbose: print 'Reading error data from %s ...' % (print_location(error_file),)
error = np.loadtxt(error_file) if error_file and os.path.isfile(error_file) else None
if verbose: print 'Reading frame data from %s ...' % (print_location(frames_file),)
frames = db_gene.snp.ld_graph.read_frames(frames_file) if frames_file else None
lam = np.loadtxt(lam_file) if lam_file and os.path.isfile(lam_file) else None
# info = ProblemInfo(p, g) if info is None else info
problem = Problem(p, g, haplotype=h, error=error, frames=frames, lam=lam)
if haplotype and info:
if verbose:
print 'Reading problem info from %s ...' % (info,)
with open(info, 'rb') as fout:
problem.info = pickle.load(fout)
return problem
def read_plink(**kwargs):
'''Load a problem from the following PLINK files:
Default Override Option Data Format
======================================================================================
prefix.pdg.tfam pedigree Pedigree adjacency PLINK TFAM
(genotyped+nongenotyped samples)
prefix.tfam pedigree_genotyped Genotyped sample pedigree
(sub-graph of the pedigree) PLINK TFAM
corresponding to prefix.tped
prefix.tped genotype Genotype data PLINK TPED
prefix.hap.tped haplotype* Haplotype data PLINK TPED
prefix.err error** Genotype errors flagged Integer array (snps x samples)
prefix.info info Problem info pickle (binary)
prefix.frm frames LD-independent SNP frames text file
prefix.lam lam*** Haplotype est. recombination rate text file
* - hap data not loaded if this option is None.
** - errors set to 0 if this file is not found or this option is set to None.
*** - data not loaded if if this file is not found.
'''
# Read input options
verbose = kwargs.get('verbose', False)
prefix = kwargs.get('prefix', '')
overrideable_option = lambda name, default: kwargs.get(
name, default if prefix else None)
pedigree = overrideable_option('pedigree', prefix + '.pdg.tfam')
pedigree_genotyped = overrideable_option('pedigree_genotyped',
prefix + '.tfam')
genotype = overrideable_option('genotype', prefix + '.tped')
haplotype = overrideable_option('haplotype', prefix + '.hap.tped')
error_file = overrideable_option('error', prefix + '.err')
info = overrideable_option('info', prefix + '.info')
if not np.all([[pedigree, pedigree_genotyped, genotype, error_file]
is not None]):
raise ValueError(
'Must specify a prefix or pedigree, pedigree_genotyped, genotype, error files'
)
frames_file = overrideable_option('frames', prefix + '.frm')
lam_file = overrideable_option('lam', prefix + '.lam')
# Load data
print_location = lambda x: x if x else '-'
if verbose:
print 'Reading pedigree from %s, %s ...' % (
print_location(pedigree),
print_location(pedigree_genotyped),
)
p = io_pedigree.read(pedigree, genotyped_id_file=pedigree_genotyped)
if verbose:
print 'Reading genotype data from %s ...' % (
print_location(genotype), )
g = io_genotype.read('plink', 'genotype', tped=genotype, load_ids=False)
if verbose:
print 'Reading haplotype data from %s ...' % (
print_location(haplotype), )
h = io_genotype.read('plink', 'haplotype', tped=haplotype,
load_ids=False) if haplotype else None
if verbose:
print 'Reading error data from %s ...' % (print_location(error_file), )
error = np.loadtxt(
error_file) if error_file and os.path.isfile(error_file) else None
if verbose:
print 'Reading frame data from %s ...' % (
print_location(frames_file), )
frames = db_gene.snp.ld_graph.read_frames(
frames_file) if frames_file else None
lam = np.loadtxt(
lam_file) if lam_file and os.path.isfile(lam_file) else None
# info = ProblemInfo(p, g) if info is None else info
problem = Problem(p, g, haplotype=h, error=error, frames=frames, lam=lam)
if haplotype and info:
if verbose:
print 'Reading problem info from %s ...' % (info, )
with open(info, 'rb') as fout:
problem.info = pickle.load(fout)
return problem
