def too_slow_test_layout_hut(self):
'''Test generating layout coordinates for the Hutterites pedigree. This test is more about
speed, to see that we do it in reasonable time.'''
p = io_pedigree.read(itu.HUTT_PED)
positions = pedigree_plot_laplacian._layout_positions(p.graph) #@UnusedVariable
# Save to file - slow
'''
def test_marriage_graph_layout_positions(self):
'''Test generating the extended graph layout position.'''
p = io_pedigree.read(itu.SMALL_FILE)
g = p.graph
g_extended = pedigree_plot_laplacian._marriage_graph(g)
assert_equal(g.number_of_nodes(), 8, 'Wrong number of nodes')
assert_equal(g.number_of_edges(), 10, 'Wrong number of edges')
assert_equal(g_extended.number_of_nodes(), 12, 'Wrong number of nodes')
assert_equal(g_extended.number_of_edges(), 13, 'Wrong number of edges')
#positions =
pedigree_plot_laplacian._layout_positions(g, g_extended)
#expected =
{
1: (-0.23562670914672229, 2),
2: (-0.063382627268225591, 3),
3: (-0.23562670914672237, 3),
4: (0.1502736499569044, 1),
5: (0.15027364995690434, 2),
6: (0.43352532974526942, 0),
7: (0.43352532974526858, 0),
8: (-0.48586913569278134, 2),
-1: (-0.054615070741569148, 2.5),
-4: (0.31358843226722749, 0.5),
-3: (-0.054615070741569086, 2.5),
-2: (-0.35145106893398231, 1.5)
}
def read_pedigree_from_test_file(file_name, genotyped_id_file=None):
'''Load a pedigree from a PLINK TFAM file.'''
data = np.genfromtxt(file_name, np.dtype(int))
p = io_pedigree.read(file_name, genotyped_id_file=genotyped_id_file)
assert_equal(p._graph.number_of_nodes(), data.shape[0], 'Incorrect number of nodes')
assert nx.is_directed_acyclic_graph(p._graph), 'Pedigree is not a DAG'
return p
def too_slow_test_layout_hut(self):
'''Test generating layout coordinates for the Hutterites pedigree. This test is more about
speed, to see that we do it in reasonable time.'''
p = io_pedigree.read(itu.HUTT_PED)
positions = pedigree_plot_laplacian._layout_positions(
p.graph) #@UnusedVariable
# Save to file - slow
'''
def read_pedigree_from_test_file(file_name, genotyped_id_file=None):
'''Load a pedigree from a PLINK TFAM file.'''
data = np.genfromtxt(file_name, np.dtype(int))
p = io_pedigree.read(file_name, genotyped_id_file=genotyped_id_file)
assert_equal(p._graph.number_of_nodes(), data.shape[0],
'Incorrect number of nodes')
assert nx.is_directed_acyclic_graph(p._graph), 'Pedigree is not a DAG'
return p
def test_save_load_pedigree_plink(self):
'''Check that saving and loading a pedigree object from file preserves the original object.'''
p = itu.Templates.pedigree_hut()
out_file = tempfile.TemporaryFile()
io_pedigree.write(p, out_file)
out_file.seek(0)
p2 = io_pedigree.read( out_file, genotyped_id_file=itu.GENOTYPE_SAMPLE+'.tfam')
out_file.close()
assert_equal(p, p2, 'Saving and loading did not restore the original pedigree')
def test_marriage_graph(self):
'''Test generating the extended graph.'''
p = io_pedigree.read(itu.HUTT_PED)
g = p.graph
g_extended = pedigree_plot_laplacian._marriage_graph(g)
assert_equal(g.number_of_nodes(), 3671, 'Wrong number of nodes')
assert_equal(g.number_of_edges(), 7200, 'Wrong number of edges')
assert_equal(g_extended.number_of_nodes(), 4661, 'Wrong number of nodes')
assert_equal(g_extended.number_of_edges(), 5580, 'Wrong number of edges')
def read(self, file_name, genotyped_id_file=None):
'''Load pedigree from file in old format.'''
p = io_pedigree.read(file_name, genotyped_id_file)
# Load data from text file a second time to read the old-study-specific-column. Not efficient.
data = np.genfromtxt(file_name, np.dtype(int))
old_generation = dict(data[:,(1,6)])
# Wrap by old pedigree object
return PedigreeOldStudy(p, old_generation)
def test_marriage_graph(self):
'''Test generating the extended graph.'''
p = io_pedigree.read(itu.HUTT_PED)
g = p.graph
g_extended = pedigree_plot_laplacian._marriage_graph(g)
assert_equal(g.number_of_nodes(), 3671, 'Wrong number of nodes')
assert_equal(g.number_of_edges(), 7200, 'Wrong number of edges')
assert_equal(g_extended.number_of_nodes(), 4661,
'Wrong number of nodes')
assert_equal(g_extended.number_of_edges(), 5580,
'Wrong number of edges')
def test_lca_small(self):
'''Test lowest common ancestor computation in a small pedigree.'''
p = io_pedigree.read(itu.SMALL_FILE)
# Direct siblings
self.__compute_and_check_lca(p, 6, 7, [4, 5], 2)
# Far siblings
u = 6
v = 8
w = self.__compute_and_check_lca(p, u, v, [3], 3)
assert_equal(shortest_path(p.graph, w, u), [3, 5, 6], 'Wrong shorted path from ancestor to node u')
assert_equal(shortest_path(p.graph, w, v), [3, 8], 'Wrong shorted path from ancestor to node v')
# No common ancestor exists
self.__compute_and_check_lca(p, 1, 2, [None], Infinity)
def test_marriage_graph_layout_positions(self):
'''Test generating the extended graph layout position.'''
p = io_pedigree.read(itu.SMALL_FILE)
g = p.graph
g_extended = pedigree_plot_laplacian._marriage_graph(g)
assert_equal(g.number_of_nodes(), 8, 'Wrong number of nodes')
assert_equal(g.number_of_edges(), 10, 'Wrong number of edges')
assert_equal(g_extended.number_of_nodes(), 12, 'Wrong number of nodes')
assert_equal(g_extended.number_of_edges(), 13, 'Wrong number of edges')
#positions =
pedigree_plot_laplacian._layout_positions(g, g_extended)
#expected =
{1: (-0.23562670914672229, 2), 2: (-0.063382627268225591, 3), 3: (-0.23562670914672237, 3), 4: (0.1502736499569044, 1), 5: (0.15027364995690434, 2), 6: (0.43352532974526942, 0), 7: (0.43352532974526858, 0), 8: (-0.48586913569278134, 2), -1: (-0.054615070741569148, 2.5), -4: (0.31358843226722749, 0.5), -3: (-0.054615070741569086, 2.5), -2: (-0.35145106893398231, 1.5)}
def test_lca_small(self):
'''Test lowest common ancestor computation in a small pedigree.'''
p = io_pedigree.read(itu.SMALL_FILE)
# Direct siblings
self.__compute_and_check_lca(p, 6, 7, [4, 5], 2)
# Far siblings
u = 6
v = 8
w = self.__compute_and_check_lca(p, u, v, [3], 3)
assert_equal(shortest_path(p.graph, w, u), [3, 5, 6],
'Wrong shorted path from ancestor to node u')
assert_equal(shortest_path(p.graph, w, v), [3, 8],
'Wrong shorted path from ancestor to node v')
# No common ancestor exists
self.__compute_and_check_lca(p, 1, 2, [None], Infinity)
def test_families(self):
'''Test family computation.'''
p = io_pedigree.read(itu.HUTT_PED)
assert_equal(len(list(pt.families(p.graph))), 990, 'Wrong number of pedigree families')
--------------------------------------------------
Main program
--------------------------------------------------
'''
options, args = __parse_command_line_args(sys.argv)
var_file_prefix, input_file, output_file = args
genotype_filter = __GENOTYPE_FILTER[options.genotype_filter]
genotype_cleaner = __GENOTYPE_CLEANER[options.genotype_filter]
allele_start_index = 1 if options.type == 'imputed' else 0
try:
# Read location list
snp_dao = SnpDao(options.db_url)
input_file = sys.stdin if args[1] == '-' else open(input_file, 'rb')
# Sample IDs are read from the pedigree, and must match the genotype files' ordering
pedigree = io_pedigree.read(options.pedigree_file,
options.genotype_id_file)
node_of = pedigree.node_of
sample_id = np.loadtxt(
options.id_file, dtype=np.int,
ndmin=1) if options.id_file else pedigree._sample_id
N = pedigree.num_genotyped
sample_index = np.array(
filter(lambda x: x is not None and x < N,
map(node_of.get, sample_id))
) # Filter FINDIVs that are not in the imputed FINDIV set
out = open(output_file, 'wb')
# Print header line
if options.output_format == 'matrix':
out.write('\t'.join([
'variant', 'chromosome', 'bp_start', 'bp_stop', 'variant_type',
def test_families(self):
'''Test family computation.'''
p = io_pedigree.read(itu.HUTT_PED)
assert_equal(len(list(pt.families(p.graph))), 990,
'Wrong number of pedigree families')
def test_lca_hut(self):
'''Test lowest common ancestor computation in a large pedigree.'''
p = io_pedigree.read(itu.HUTT_PED)
self.__compute_and_check_lca(p, 169512, 170362, [8551], 9)
--------------------------------------------------
Main program
--------------------------------------------------
'''
options, args = __parse_command_line_args(sys.argv)
var_file_prefix, input_file, output_file = args
genotype_filter = __GENOTYPE_FILTER[options.genotype_filter]
genotype_cleaner = __GENOTYPE_CLEANER[options.genotype_filter]
allele_start_index = 1 if options.type == 'imputed' else 0
try:
# Read location list
snp_dao = SnpDao(options.db_url)
input_file = sys.stdin if args[1] == '-' else open(input_file, 'rb')
# Sample IDs are read from the pedigree, and must match the genotype files' ordering
pedigree = io_pedigree.read(options.pedigree_file, options.genotype_id_file)
node_of = pedigree.node_of
sample_id = np.loadtxt(options.id_file, dtype=np.int, ndmin=1) if options.id_file else pedigree._sample_id
N = pedigree.num_genotyped
sample_index = np.array(filter(lambda x: x is not None and x < N, map(node_of.get, sample_id))) # Filter FINDIVs that are not in the imputed FINDIV set
out = open(output_file, 'wb')
# Print header line
if options.output_format == 'matrix':
out.write('\t'.join(['variant', 'chromosome', 'bp_start', 'bp_stop', 'variant_type', 'ref_allele', 'minor_allele'] + map(str, sample_id)) + '\n')
# Extract data using tabix for each location. A location may be a range of bps and may
# correspond to multiple output lines.
snp_count = [0, 0, 0, 0, 0] # #found variants; #not-found variants; #multiply-matching variants; #nameless variants
# print list(enumerate(it.chain.from_iterable(__parse_line(line, snp_dao, debug=options.debug)
# for line in (line.rstrip('\n').rstrip('\r')
def test_lca_hut(self):
'''Test lowest common ancestor computation in a large pedigree.'''
p = io_pedigree.read(itu.HUTT_PED)
self.__compute_and_check_lca(p, 169512, 170362, [8551], 9)
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
