本文整理汇总了Python中Population.Population.tag_list方法的典型用法代码示例。如果您正苦于以下问题：Python Population.tag_list方法的具体用法？Python Population.tag_list怎么用？Python Population.tag_list使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Population.Population的用法示例。
在下文中一共展示了Population.tag_list方法的5个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: pos_dict
# 需要导入模块: from Population import Population [as 别名]
# 或者: from Population.Population import tag_list [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示例2: Population
# 需要导入模块: from Population import Population [as 别名]
# 或者: from Population.Population import tag_list [as 别名]
################################################################################
prog = 'coverage'
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)示例3: Population
# 需要导入模块: from Population import Population [as 别名]
# 或者: from Population.Population import tag_list [as 别名]
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':
column, name = tag.split(':')
tag = '{0}:{1}'.format(int(column) - 2, name)
args.append(tag)
gd_util.run_program(prog, args)
# kinship.map
# kinship.ped
# kinship.dat
################################################################################
prog = 'king'
示例4: Population
# 需要导入模块: from Population import Population [as 别名]
# 或者: from Population.Population import tag_list [as 别名]
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')
################################################################################
prog = 'admix_prep'
args = [ prog ]示例5: Population
# 需要导入模块: from Population import Population [as 别名]
# 或者: from Population.Population import tag_list [as 别名]
if not p_total.is_superset(p1):
gd_util.die('There is an individual in the first population 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 the second population that is not in the SNP table')
################################################################################
prog = 'offspring_heterozygosity'
args = [ prog ]
args.append(input) # a Galaxy SNP table
for tag in p1.tag_list():
column, name = tag.split(':')
if input_type == 'gd_genotype':
column = int(column) - 2
tag = '{0}:{1}:{2}'.format(column, 0, name)
args.append(tag)
for tag in p2.tag_list():
column, name = tag.split(':')
if input_type == 'gd_genotype':
column = int(column) - 2
tag = '{0}:{1}:{2}'.format(column, 1, name)