Python Population.from_population_file方法代码示例

# 需要导入模块: from Population import Population [as 别名]
# 或者: from Population.Population import from_population_file [as 别名]
def pos_dict(gd_indivs_file, input_type):
    rv = {}

    p = Population()
    p.from_population_file(gd_indivs_file)

    for tag in p.tag_list():
        column, name = tag.split(':')
        column = int(column) - 1

        if input_type == 'gd_genotype':
            column -= 2

        rv[name] = column

    return rv

# 需要导入模块: from Population import Population [as 别名]
# 或者: from Population.Population import from_population_file [as 别名]
import gd_util
import sys
from Population import Population

################################################################################

if len(sys.argv) != 13:
    gd_util.die('Usage')

input, p1_input, p2_input, input_type, data_source, min_reads, min_qual, retain, discard_fixed, biased, output, ind_arg = sys.argv[1:]

p_total = Population()
p_total.from_wrapped_dict(ind_arg)

p1 = Population()
p1.from_population_file(p1_input)
if not p_total.is_superset(p1):
    gd_util.die('There is an individual in population 1 that is not in the SNP table')

p2 = Population()
p2.from_population_file(p2_input)
if not p_total.is_superset(p2):
    gd_util.die('There is an individual in population 2 that is not in the SNP table')

################################################################################

prog = 'Fst_column'

args = [ prog ]
args.append(input)
args.append(data_source)

# 需要导入模块: from Population import Population [as 别名]
# 或者: from Population.Population import from_population_file [as 别名]
        if p_type == 'gd_genotype':
            column = int(column) - 2
        the_list.append('{0}:{1}:{2}'.format(val, column, name))

################################################################################

if len(sys.argv) != 11:
    gd_util.die('Usage')

snp_input, snp_ext, snp_arg, cov_input, cov_ext, cov_arg, indiv_input, min_coverage, req_thresh, output = sys.argv[1:]

p_snp = load_pop(snp_input, snp_arg)
p_cov = load_pop(cov_input, cov_arg)

p_ind = Population()
p_ind.from_population_file(indiv_input)

if not p_snp.is_superset(p_ind):
  gd_util.die('There is an individual in the population individuals that is not in the SNP/Genotype table')

if p_cov is not None and (not p_cov.is_superset(p_ind)):
  gd_util.die('There is an individual in the population individuals that is not in the Coverage table')

################################################################################

prog = 'mito_pi'

args = [ prog ]
args.append(snp_input)
args.append(cov_input)
args.append(min_coverage)

# 需要导入模块: from Population import Population [as 别名]
# 或者: from Population.Population import from_population_file [as 别名]
def load_and_check_pop(name, file, total_pop):
    p = Population(name=name)
    p.from_population_file(file)
    if not total_pop.is_superset(p):
        gd_util.die('There is an individual in {0} that is not in the SNP table'.format(name))
    return p

# 需要导入模块: from Population import Population [as 别名]
# 或者: from Population.Population import from_population_file [as 别名]
args = [ prog ]
args.append(input)
args.append(data_source)

user_coverage_file = os.path.join(extra_files_path, 'coverage.txt')
args.append(user_coverage_file)

population_list = []

if all_individuals:
    tags = p_total.tag_list()
elif p1_input is not None:
    p1 = Population()
    this_pop = Population()
    this_pop.from_population_file(p1_input)
    population_list.append(this_pop)
    p1.from_population_file(p1_input)
    if not p_total.is_superset(p1):
        gd_util.die('There is an individual in the population that is not in the SNP table')
    tags = p1.tag_list()
else:
    tags = []
    for population_file, population_name in population_info:
        population = Population()
        this_pop = Population()
        this_pop.from_population_file(population_file)
        population_list.append(this_pop)
        population.from_population_file(population_file)
        if not p_total.is_superset(population):
            gd_util.die('There is an individual in the {} population that is not in the SNP table'.format(population_name))

# 需要导入模块: from Population import Population [as 别名]
# 或者: from Population.Population import from_population_file [as 别名]
import gd_util

from Population import Population

################################################################################

if len(sys.argv) != 6:
    gd_util.die('Usage')

input, input_type, ind_arg, pop_input, output = sys.argv[1:]

p_total = Population()
p_total.from_wrapped_dict(ind_arg)

p1 = Population()
p1.from_population_file(pop_input)
if not p_total.is_superset(p1):
    gd_util.die('There is an individual in the population that is not in the SNP table')

################################################################################

prog = 'kinship_prep'

args = [ prog ]
args.append(input)  # a Galaxy SNP table
args.append(0)      # required number of reads for each individual to use a SNP
args.append(0)      # required genotype quality for each individual to use a SNP
args.append(0)      # minimum spacing between SNPs on the same scaffold

for tag in p1.tag_list():
    if input_type == 'gd_genotype':

# 需要导入模块: from Population import Population [as 别名]
# 或者: from Population.Population import from_population_file [as 别名]
p_total = Population()
p_total.from_wrapped_dict(ind_arg)

individual_population = {}
population_list = []

if all_individuals:
    p1 = p_total
    p1.name = 'All Individuals'
    population_list.append(p1)
else:
    p1 = Population()
    for file, name in population_files:
        this_pop = Population(name)
        this_pop.from_population_file(file)
        population_list.append(this_pop)

        for tag in this_pop.tag_list():
            if tag not in individual_population:
                individual_population[tag] = name

        # add individuals from this file to p1
        p1.from_population_file(file)


if not p_total.is_superset(p1):
    gd_util.die('There is an individual in the population that is not in the SNP table')

################################################################################

# 需要导入模块: from Population import Population [as 别名]
# 或者: from Population.Population import from_population_file [as 别名]
import gd_util
import sys
from Population import Population

################################################################################

if len(sys.argv) != 7:
    gd_util.die('Usage')

gd_saps_file, gd_snps_file, covered_intervals_file, gd_indivs_file, output_file, ind_arg = sys.argv[1:]

p_total = Population()
p_total.from_wrapped_dict(ind_arg)

p1 = Population()
p1.from_population_file(gd_indivs_file)
if not p_total.is_superset(p1):
    gd_util.die('There is an individual in the population individuals that is not in the SNP table')

################################################################################

prog = 'get_pi'

args = [ prog ]
args.append(gd_saps_file)
args.append(gd_snps_file)
args.append(covered_intervals_file)

columns = p1.column_list()
for column in columns:
    args.append(column)