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')