comparison dpmix.py @ 31:a631c2f6d913

Update to Miller Lab devshed revision 3c4110ffacc3

30:4188853b940b

from Population import Population
import gd_composite
from dpmix_plot import make_dpmix_plot
from LocationFile import LocationFile

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

if len(sys.argv) != 22:
    print "usage"
    sys.exit(1)

input, input_type, data_source, switch_penalty, ap1_input, ap1_name, ap2_input, ap2_name, ap3_input, ap3_name, p_input, output, output2, output2_dir, dbkey, ref_column, galaxy_data_index_dir, heterochromatin_loc_file, ind_arg, het_arg, add_logs = sys.argv[1:]

if ap3_input == '/dev/null':
    populations = 2
else:
    populations = 3

population_list = []

p_total = Population()
p_total.from_wrapped_dict(ind_arg)

ap1 = Population(name='Ancestral population 1')
ap1.from_population_file(ap1_input)
population_list.append(ap1)
if not p_total.is_superset(ap1):
    gd_util.die('There is an individual in ancestral population 1 that is not in the SNP table')

ap2 = Population(name='Ancestral population 2')
ap2.from_population_file(ap2_input)
population_list.append(ap2)
if not p_total.is_superset(ap2):
    gd_util.die('There is an individual in ancestral population 2 that is not in the SNP table')

if populations == 3:
    ap3 = Population(name='Ancestral population 3')
    ap3.from_population_file(ap3_input)
    population_list.append(ap3)
    if not p_total.is_superset(ap3):
        gd_util.die('There is an individual in ancestral population 3 that is not in the SNP table')

p = Population(name='Potentially admixed')
p.from_population_file(p_input)
population_list.append(p)
if not p_total.is_superset(p):
    gd_util.die('There is an individual in the population that is not in the SNP table')

gd_util.mkdir_p(output2_dir)

################################################################################
# Create tabular file

args.append(add_logs)
args.append(switch_penalty)
args.append(heterochrom_path)
args.append(misc_file)

columns = ap1.column_list()
for column in columns:
    col = int(column)
    name = ap1.individual_with_column(column).name
    first_token = name.split()[0]
    if input_type == 'gd_genotype':
        col -= 2
    args.append('{0}:1:{1}'.format(col, first_token))

columns = ap2.column_list()
for column in columns:
    col = int(column)
    name = ap2.individual_with_column(column).name
    first_token = name.split()[0]
    if input_type == 'gd_genotype':
        col -= 2
    args.append('{0}:2:{1}'.format(col, first_token))

if populations == 3:
    columns = ap3.column_list()
    for column in columns:
        col = int(column)
        name = ap3.individual_with_column(column).name
        first_token = name.split()[0]
        if input_type == 'gd_genotype':
            col -= 2
        args.append('{0}:3:{1}'.format(col, first_token))

columns = p.column_list()
for column in columns:
    col = int(column)
    name = p.individual_with_column(column).name
    first_token = name.split()[0]
    if input_type == 'gd_genotype':
        col -= 2
    args.append('{0}:0:{1}'.format(col, first_token))

with open(output, 'w') as fh:
    gd_util.run_program(prog, args, stdout=fh)

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

31:a631c2f6d913

from Population import Population
import gd_composite
from dpmix_plot import make_dpmix_plot
from LocationFile import LocationFile

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

def append_pop_tags(the_list, p, input_type, number):
    for tag in p.tag_list():
        column, name = tag.split(':')
        if input_type == 'gd_genotype':
            column = int(column) - 2
        the_list.append('{0}:{1}:{2}'.format(column, number, name))

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

if len(sys.argv) != 22:
    print "usage"
    sys.exit(1)

input, input_type, data_source, switch_penalty, ap1_input, ap1_name, ap2_input, ap2_name, ap3_input, ap3_name, p_input, output, output2, output2_dir, dbkey, ref_column, galaxy_data_index_dir, heterochromatin_loc_file, ind_arg, het_arg, add_logs = sys.argv[1:]

if ap1_input == '/dev/null':
    use_reference = True
else:
    use_reference = False

if ap3_input == '/dev/null':
    populations = 2
else:
    populations = 3

population_list = []

p_total = Population()
p_total.from_wrapped_dict(ind_arg)

if not use_reference:
    ap1 = load_and_check_pop('Ancestral population 1', ap1_input, p_total)
    population_list.append(ap1)

ap2 = load_and_check_pop('Ancestral population 2', ap2_input, p_total)
population_list.append(ap2)

if populations == 3:
    ap3 = load_and_check_pop('Ancestral population 3', ap3_input, p_total)
    population_list.append(ap3)

p = load_and_check_pop('Potentially admixed', p_input, p_total)
population_list.append(p)

gd_util.mkdir_p(output2_dir)

################################################################################
# Create tabular file

args.append(add_logs)
args.append(switch_penalty)
args.append(heterochrom_path)
args.append(misc_file)

if use_reference:
    args.append('0:1:reference')
else:
    append_pop_tags(args, ap1, input_type, 1)

append_pop_tags(args, ap2, input_type, 2)

if populations == 3:
    append_pop_tags(args, ap3, input_type, 3)

append_pop_tags(args, p, input_type, 0)

with open(output, 'w') as fh:
    gd_util.run_program(prog, args, stdout=fh)

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