def read_beagle_markerfile(filename, label=None):
"""
Reads marker locations from a BEAGLE formatted file
:param filename: The file to be read
:param label: An optional label to give the chromosome, since the BEAGLE
format does not require it
:type filename: string
:rtype: ChromosomeTemplate
"""
with smartopen(filename) as f:
chrom = ChromosomeTemplate(label=label)
last_pos = -1
for line in f:
rec = BeagleMarkerRecord(line)
if rec.pos < 0:
raise FileFormatError(
'Bad position for genotype: {}'.format(rec.pos))
elif rec.pos <= last_pos:
raise FileFormatError('Makers in file out of order')
chrom.add_genotype(None, map_position=None, label=rec.label,
bp=rec.pos, reference=rec.reference,
alternates=rec.alternates)
last_pos = rec.pos
return chrom
def test_labelledallele_delabeler():
ngenos = 10 # Number of genotypes per chromosome
if ngenos % 2 == 1:
raise ValueError('Even number of genotypes needed')
p = Population()
c = ChromosomeTemplate()
for i in range(ngenos):
c.add_genotype()
p.add_chromosome(c)
a = Individual(p, 1)
a._init_genotypes(blankchroms=False)
a.genotypes[0][0] = Alleles([1]*ngenos)
a.genotypes[0][1] = Alleles([2]*ngenos)
b = Individual(p, 2)
b._init_genotypes(blankchroms=False)
b.genotypes[0][0] = Alleles([3] * ngenos)
b.genotypes[0][1] = Alleles([4] * ngenos)
chromatid_spans = [InheritanceSpan(a, 0, 0, 0, ngenos//2),
InheritanceSpan(b, 0, 1, ngenos//2, ngenos)]
chromatid = LabelledAlleles(spans=chromatid_spans, chromobj=c)
expected_value = [1]*(ngenos//2) + [4] * (ngenos//2)
expected_value = Alleles(expected_value)
actual_value = chromatid.delabel()
assert all(actual_value == expected_value)
def read_map(filename, only=None):
with open(filename) as f:
line = f.readline()
header = line.strip().split()
sex_specific_map = len(header) == 5
lastchrom = None
chromosomes = []
for markernum, line in enumerate(f):
l = line.strip().split()
if sex_specific_map:
chrom, marker, pos, male_pos, female_pos = l
else:
chrom, marker, pos = l
if only and marker not in only:
continue
pos = float(pos)
if chrom != lastchrom:
if lastchrom:
c.finalize()
c = ChromosomeTemplate(label=chrom)
chromosomes.append(c)
lastchrom = chrom
c.add_genotype(map_position=pos, label=marker)
for chrom in chromosomes:
chrom.finalize()
return chromosomes
def read_map(mapfile):
"""
Reads a PLINK map file into a list of ChromosomeTemplate objects
Arguments:
mapfile: The file to be read
Returns: a list of ChromosomeTemplate objects
"""
last_chr, last_pos = None, 0
chroms = []
chromosome = None
with open(mapfile) as f:
for i, line in enumerate(f):
line = line.strip().split()
chr, label, cm, pos = line
cm, pos = float(cm), int(pos)
if pos < 0:
raise FileFormatError("Invalid position: {}".format(pos))
if chr != last_chr:
# If this happens, we've moved on to a new chromosome,
# or we've just started. If we haven't just started, We'll
# close up the old one
if i > 0:
chromosome.finalize()
chroms.append(chromosome)
# Make the next chromosome
chromosome = ChromosomeTemplate(label=chr)
elif pos < last_pos:
raise FileFormatError("Map file not sorted")
chromosome.add_genotype(None, cm, label=label, bp=pos)
last_chr, last_pos = chr, pos
chromosome.finalize()
chroms.append(chromosome)
return chroms
def read_beagle_markerfile(filename, label=None):
"""
Reads marker locations from a BEAGLE formatted file
:param filename: The file to be read
:param label: An optional label to give the chromosome, since the BEAGLE
format does not require it
:type filename: string
:rtype: ChromosomeTemplate
"""
with smartopen(filename) as f:
chrom = ChromosomeTemplate(label=label)
last_pos = -1
for line in f:
rec = BeagleMarkerRecord(line)
if rec.pos < 0:
raise FileFormatError('Bad position for genotype: {}'.format(
rec.pos))
elif rec.pos <= last_pos:
raise FileFormatError('Makers in file out of order')
chrom.add_genotype(None,
map_position=None,
label=rec.label,
bp=rec.pos,
reference=rec.reference,
alternates=rec.alternates)
last_pos = rec.pos
return chrom
def read_beagle_markerfile(filename, label=None):
'''
Reads marker locations from a beagle format file
Arguments
-----
filename: The file to be read
label: An optional label to give the chromosome, since the BEAGLE
format does not require it
Returns: a ChromosomeTemplate object
'''
with open(filename) as f:
chrom = ChromosomeTemplate(label=label)
last_pos = -1
for line in f:
rec = BeagleMarkerRecord(line)
if rec.pos < 0:
raise FileFormatError(
'Bad position for genotype: {}'.format(rec.pos))
elif rec.pos <= last_pos:
raise FileFormatError('Makers in file out of order')
chrom.add_genotype(None, cm=None, label=rec.label, bp=rec.pos,
reference=rec.reference, alternates=rec.alternates)
last_pos = rec.pos
return chrom
def test_labelledallele_delabeler():
ngenos = 10 # Number of genotypes per chromosome
if ngenos % 2 == 1:
raise ValueError('Even number of genotypes needed')
p = Population()
c = ChromosomeTemplate()
for i in range(ngenos):
c.add_genotype()
p.add_chromosome(c)
a = Individual(p, 1)
a._init_genotypes(blankchroms=False)
a.genotypes[0][0] = Alleles([1] * ngenos)
a.genotypes[0][1] = Alleles([2] * ngenos)
b = Individual(p, 2)
b._init_genotypes(blankchroms=False)
b.genotypes[0][0] = Alleles([3] * ngenos)
b.genotypes[0][1] = Alleles([4] * ngenos)
chromatid_spans = [
InheritanceSpan(a, 0, 0, 0, ngenos // 2),
InheritanceSpan(b, 0, 1, ngenos // 2, ngenos)
]
chromatid = LabelledAlleles(spans=chromatid_spans, chromobj=c)
expected_value = [1] * (ngenos // 2) + [4] * (ngenos // 2)
expected_value = Alleles(expected_value)
actual_value = chromatid.delabel()
assert all(actual_value == expected_value)
def test_labelledalleles():
IS = InheritanceSpan
ngenos = 50
p = Population()
c = ChromosomeTemplate()
for i in range(ngenos):
c.add_genotype()
p.add_chromosome(c)
a = Individual(p, 1)
actual = LabelledAlleles.founder_chromosome(a, 0, 0, chromobj=c)
expected = LabelledAlleles(spans=[IS(a, 0, 0, 0, ngenos)], chromobj=c)
assert actual == expected
def test_labelledalleles():
IS = InheritanceSpan
ngenos = 50
p = Population()
c = ChromosomeTemplate()
for i in range(ngenos):
c.add_genotype()
p.add_chromosome(c)
a = Individual(p, 1)
actual = LabelledAlleles.founder_chromosome(a, 0, 0, chromobj=c)
expected = LabelledAlleles(spans=[IS(a, 0, 0, 0, ngenos)], chromobj=c)
assert actual == expected
def test_chromosometemplate():
# Test the marker finder
c = ChromosomeTemplate()
for i in range(1, 100):
c.add_genotype(map_position=i, bp=(i * 1e6))
assert c.closest_marker(0) == 0
assert c.closest_marker(5000001) == 4
assert c.closest_marker(5999999) == 5
assert c.closest_marker(1e10) == c.nmark() - 1
def add_dummy_polygene_chromosomes(self,
population,
nloc,
mean=0,
sd=1,
freqs=None,
polylabel='Polygene'):
"""
Creates many independently segregating chromosomes that
additively influence the trait.
:param population: The population to add the chromosomes to
:param nloc: The number of dummy chromosomes to create
:param mean: Mean locus additive effect
:param sd: Standard deviation of locus additive effect
:param freqs: frequencies of each polygene
:param polylabel: Label to add give chromosome
:type nloc: integer
:type mean: float
:type sd: float
:type freqs: sequence of floats
:type polylabel: string
:rtype: void
"""
if freqs is None:
freqs = np.zeros(nloc, dtype=np.float) + 0.5
if sd == 0:
effects = [mean] * nloc
else:
effects = np.random.normal(mean, sd, nloc)
for i, effect in enumerate(effects):
# Create the chromosome
lab = '{}{}'.format(polylabel, i)
c = ChromosomeTemplate(label=lab)
c.add_genotype(freqs[i], 0)
population.add_chromosome(c)
# Add the effect
locus = i, 0
self.add_effect(locus, a=effect, k=0)
def add_dummy_polygene_chromosomes(self, population, nloc,
mean=0,
sd=1,
freqs=None,
polylabel='Polygene'):
"""
Creates many independently segregating chromosomes that
additively influence the trait.
:param population: The population to add the chromosomes to
:param nloc: The number of dummy chromosomes to create
:param mean: Mean locus additive effect
:param sd: Standard deviation of locus additive effect
:param freqs: frequencies of each polygene
:param polylabel: Label to add give chromosome
:type nloc: integer
:type mean: float
:type sd: float
:type freqs: sequence of floats
:type polylabel: string
:rtype: void
"""
if freqs is None:
freqs = np.zeros(nloc, dtype=np.float) + 0.5
if sd == 0:
effects = [mean] * nloc
else:
effects = np.random.normal(mean, sd, nloc)
for i, effect in enumerate(effects):
# Create the chromosome
lab = '{}{}'.format(polylabel, i)
c = ChromosomeTemplate(label=lab)
c.add_genotype(freqs[i], 0)
population.add_chromosome(c)
# Add the effect
locus = i, 0
self.add_effect(locus, a=effect, k=0)
def test_chromosometemplate(): # Test the marker finder c = ChromosomeTemplate() for i in range(1,100): c.add_genotype(map_position=i, bp=(i*1e6)) assert c.closest_marker(0) == 0 assert c.closest_marker(5000001) == 4 assert c.closest_marker(5999999) == 5 assert c.closest_marker(1e10) == c.nmark() - 1
def read_map(mapfile):
"""
Reads a PLINK map file into a list of ChromosomeTemplate objects
:param mapfile: Path of the file to be read
:type mapfile: string
:rtype: a list of ChromosomeTemplate objects
"""
last_chr, last_pos = None, 0
chroms = ChromosomeSet()
chromosome = None
with smartopen(mapfile) as f:
for i, line in enumerate(f):
line = line.strip().split()
chrom, label, cm, pos = line
cm, pos = float(cm), int(pos)
if pos < 0:
raise FileFormatError('Invalid position: {}'.format(pos))
if chrom != last_chr:
# If this happens, we've moved on to a new chromosome,
# or we've just started. If we haven't just started, We'll
# close up the old one
if i > 0:
chromosome.finalize()
chroms.add_chromosome(chromosome)
# Make the next chromosome
chromosome = ChromosomeTemplate(label=chrom)
elif pos < last_pos:
raise FileFormatError('Map file not sorted')
chromosome.add_genotype(None, cm, label=label, bp=pos)
last_chr, last_pos = chrom, pos
chromosome.finalize()
chroms.add_chromosome(chromosome)
return chroms
def blank_chromosome(size=2):
ch = ChromosomeTemplate()
for i in range(size):
ch.add_genotype()
return ch
def blank_chromosome(size=2):
ch = ChromosomeTemplate()
for i in range(size):
ch.add_genotype()
return ch
def read_vcf(filename, require_pass=False, freq_info=None):
"""
Reads a VCF file and returns a Population object with the
individuals represented in the file
Genotypes generated by this function will be sparse
:param require_pass: only allow variants with PASS under FILTER
:type require_pass: bool
:param freq_info: INFO field to get allele frequency from
:param freq_info: string
:returns: Individuals in the VCF
:rtype: Population
"""
with smartopen(filename) as f:
genotypes = []
pop, inds = _vcf_parseheader(f)
last_chrom = None
chromobj = None
for line in f:
record = VCFRecord(line)
if require_pass and not record.filter_passed:
continue
if record.chrom != last_chrom:
if last_chrom is not None:
pop.add_chromosome(chromobj)
chromobj = ChromosomeTemplate(label=record.chrom)
if freq_info is not None:
freq = _vcf_get_infofreq(record.info, freq_info)
else:
freq = 0
genorow = record.genotypes()
genotypes.append(genorow)
chromobj.add_genotype(bp=record.pos,
label=record.label,
frequency=freq)
last_chrom = record.chrom
pop.add_chromosome(chromobj)
pop.chromosomes.finalize()
for ind in inds:
# Initialize new genotypes
ind._init_genotypes(sparse=True)
# Now actually sift through markers and assign them to individuals
final_indices = []
for chromidx, chromobj in enumerate(pop.chromosomes):
indices = zip([chromidx] * chromobj.nmark(), range(chromobj.nmark()))
final_indices.extend(indices)
raw_indices = range(len(genotypes))
for raw, final in zip(raw_indices, final_indices):
chromidx, markidx = final
row = genotypes[raw]
assign_genorow(row, inds, chromidx, markidx)
# Kill the row so we don't end up with the whole dataset in memory twice
genotypes[raw] = None
return pop
def read_vcf(filename, require_pass=False, freq_info=None, info_filters=None):
'''
Reads a VCF file and returns a Population object with the
individuals represented in the file
'''
if not info_filters:
info_filters = []
for filter in info_filters:
if not callable(filter):
raise ValueError('Filter not callable')
with open(filename) as f:
pop = Population()
last_chrom = None
genotypes = []
for i, line in enumerate(f):
if line.startswith('##'):
continue
elif line.startswith('#'):
ind_ids = line.strip().split()[9:]
inds = [Individual(pop, ind_id) for ind_id in ind_ids]
for ind in inds:
pop.register_individual(ind)
break
for i, line in enumerate(f):
record = VCFRecord(line)
if info_filters and not all(filter(record) for filter in info_filters):
continue
if require_pass and not record.filter_passed:
continue
if record.chrom != last_chrom:
if last_chrom is not None:
chromobj.finalize()
pop.add_chromosome(chromobj)
chromobj = ChromosomeTemplate(label=record.chrom)
if freq_info is not None and freq_info in record.info:
freq = record.info[freq_info]
if ',' in freq:
freq = freq.split(',')[0]
freq = float(freq)
else:
freq = 0
genorow = record.genotypes()
genotypes.append(genorow)
chromobj.add_genotype(bp=record.pos,
label=record.label,
frequency=freq)
last_chrom = record.chrom
chromobj.finalize()
pop.add_chromosome(chromobj)
for ind in inds:
# Initialize new genotypes
ind._init_genotypes(sparse=True)
# Now actually sift through markers and assign them to individuals
final_indices = []
for chromidx, chromobj in enumerate(pop.chromosomes):
indices = zip([chromidx]*chromobj.nmark(), range(chromobj.nmark()))
final_indices.extend(indices)
raw_indices = range(len(genotypes))
for raw, final in zip(raw_indices, final_indices):
chromidx, markidx = final
row = genotypes[raw]
assign_genorow(row, inds, chromidx, markidx)
# Kill the row so we don't end up with the whole dataset in memory twice
genotypes[raw] = None
return pop
