def run_vcf_to_sampler(f_in, f_out):
args = [
starting_files[0], '--statistic-file', f_in, '--sample-size', '20',
'--random-seed', '1000', '--overwrite'
]
print(args)
vcf_sampler.run(args)
def run_vcf_to_sampler(f_in, f_out):
args = [
'merged_chr1_10000.vcf.gz', '--statistic-file',
'merged_chr1_10000.Tajima.D', '--out-prefix', 'merged_chr1_10000',
'--sample-size', '10', '--random-seed', '1000', '--overwrite'
]
vcf_sampler.run(args)
def run_vcf_to_sampler1(f_in, f_out):
args = [
starting_files[0], '--statistic-file', f_in, '--sample-size', '20',
'--random-seed', '1000', '--sample-file', 'sampled_data1.tsv',
'--out-dir', 'Sample_Files1', '--out-prefix', 'Sample1', '--overwrite'
]
print(args)
vcf_sampler.run(args)
def run_vcf_to_sampler8(f_in, f_out):
args = [
starting_files[0], '--statistic-file', f_in, '--calc-statistic',
'TajimaD', '--sample-size', '20', '--random-seed', '1000',
'--sample-file', 'sampled_data_9.tsv', '--out-dir', 'Sample_Files_9',
'--out-prefix', 'Sample_9', '--overwrite'
]
#print (args)
vcf_sampler.run(args)
def run_vcf_to_sampler2(f_in, f_out):
args = [
starting_files[0], '--statistic-file', f_in, '--calc-statistic',
'windowed-weir-fst', '--sample-size', '20', '--random-seed', '1000',
'--sample-file', 'sampled_data_3.tsv', '--out-dir', 'Sample_Files_3',
'--out-prefix', 'Sample_3', '--overwrite'
]
#print (args)
vcf_sampler.run(args)
def run_vcf_to_sampler1(f_in,f_out):
for i in range(len(list3)):
print (len(list3))
args = statFilter[i]
print (args)
vcf_sampler.run(args)
print ('hello')
print (newpath[i])
shutil.move('sampled_data.tsv', newpath[i])
shutil.move('Sample_Files', newpath[i])
shutil.move('/home/staff/asukeshkall/Downloads/Test-3/merged_chr1_10000.recode.bcf','/home/staff/asukeshkall/Downloads/Test-3/Run/test1')
shutil.move('/home/staff/asukeshkall/Downloads/Test-3/merged_chr1_10000.windowed.weir.fst','/home/staff/asukeshkall/Downloads/Test-3/Run/test2')
def run_vcf_to_sampler(f_in,f_out):
for i in range(len(list3)):
print (len(list3))
args = statFilter[i]
print (args)
vcf_sampler.run(args)
print ('hello')
print (newpath[i])
shutil.move('sampled_data.tsv', newpath[i])
shutil.move('Sample_Files', newpath[i])
shutil.move('/home/staff/asukeshkall/Downloads/Test-3/merged_chr1_10000.recode.bcf','/home/staff/asukeshkall/Downloads/Test-3/Run/test1')
shutil.move('/home/staff/asukeshkall/Downloads/Test-3/merged_chr1_10000.windowed.weir.fst','/home/staff/asukeshkall/Downloads/Test-3/Run/test1')
#shutil.move('/home/staff/asukeshkall/Downloads/Test-3/merged_chr1_10000.recode.bcf','/home/staff/asukeshkall/Downloads/Test-3/Run/'+folder)
#shutil.move('/home/staff/asukeshkall/Downloads/Test-3/merged_chr1_10000.windowed.weir.fst','/home/staff/asukeshkall/Downloads/Test-3/Run/'+folder)
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test1/merged_chr1_10000.recode.bcf')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test1/merged_chr1_10000.recode.bcf.log')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test2/merged_chr1_10000.recode.bcf')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test2/merged_chr1_10000.recode.bcf.log')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test3/merged_chr1_10000.recode.bcf')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test3/merged_chr1_10000.recode.bcf.log')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test4/merged_chr1_10000.recode.bcf')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test4/merged_chr1_10000.recode.bcf.log')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test1/merged_chr1_10000.windowed.weir.fst')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test1/merged_chr1_10000.windowed.weir.fst.log')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test2/merged_chr1_10000.windowed.weir.fst')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test2/merged_chr1_10000.windowed.weir.fst.log')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test3/merged_chr1_10000.windowed.weir.fst')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test3/merged_chr1_10000.windowed.weir.fst.log')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test4/merged_chr1_10000.windowed.weir.fst')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test4/merged_chr1_10000.windowed.weir.fst.log')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test1/sampled_data.tsv')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test2/sampled_data.tsv')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test3/sampled_data.tsv')
os.remove('/home/staff/asukeshkall/Downloads/Test-3/Run/test4/sampled_data.tsv')
shutil.rmtree('/home/staff/asukeshkall/Downloads/Test-3/Run/test1/Sample_Files')
shutil.rmtree('/home/staff/asukeshkall/Downloads/Test-3/Run/test2/Sample_Files')
shutil.rmtree('/home/staff/asukeshkall/Downloads/Test-3/Run/test3/Sample_Files')
shutil.rmtree('/home/staff/asukeshkall/Downloads/Test-3/Run/test4/Sample_Files')
def run_vcf_to_sampler(f_in,f_out):
args = statFilter[7]
print args
vcf_sampler.run(args)
def test_calc_run_1(self):
for i in range(1, 80):
os.makedirs(os.path.join('Run', 'test' + str(i)))
#================================================# Generate all combinations #=======================================================================#
comb = []
a = [['merged_chr1_10000.vcf.gz'], ['--model-file', 'input.model'],
['--model', '2Pop'],
['--statistic-file', 'merged_chr1_10000.windowed.weir.fst'],
['--sample-file', 'sampled_data.tsv'],
['--out-dir', 'Sample_Files'], ['--out-prefix', 'Sample'],
['--out-format', 'vcf.gz'], ['--overwrite'],
['--calc-statistic', 'windowed-weir-fst'],
['--statistic-window-size', '10000'],
['--sampling-scheme', 'random'], ['--uniform-bins', '10'],
['--sample-size', '10'], ['--random-seed', '456']]
for i in range(len(a)):
b = list(combinations(a, i + 1))
c = map(list, b)
comb.append(c)
whole_list = []
for x in comb:
for y in x:
b = list(itertools.chain.from_iterable(y))
whole_list.append(b)
#print b
m = whole_list
#print m
#=============================================# Filter level 1 function #========================================================================#
filList1 = []
filList2 = []
filList3 = []
def filFunc(name, lol, listname):
for x in lol:
for y in x:
if y == name:
listname.append(x)
#=====================================================================================================================#
filFunc('merged_chr1_10000.vcf.gz', m, filList1)
fnameFilter = filList1
#for t in fnameFilter:
# print t
#print "--------------"
filFunc('merged_chr1_10000.windowed.weir.fst', fnameFilter, filList2)
statFilter = filList2
print len(statFilter)
#for t in statFilter:
#print t
#print "--------------"
for i in range(len(statFilter)):
print i, statFilter[i]
vcf_sampler.run(statFilter[i])
self.assertTrue(os.path.isfile('sampled_data.tsv'))
self.assertTrue(os.path.isdir('Sample_Files'))
os.remove('sampled_data.tsv')
shutil.rmtree('Sample_Files')