def test_filter_run_9(self): newpath= "/home/staff/asukeshkall/Downloads/Test/Run/test_9" if not os.path.exists(newpath): os.makedirs(newpath) vcf_filter.run(['merged_chr1_1000.vcf.gz', '--out', 'res', '--out-format','vcf', '--filter-max-alleles', '4']) # Confirm that the output is what is expected self.assertTrue(os.path.isfile('res.filter.log')) self.assertTrue(os.path.isfile('res.recode.vcf')) # Move the files to the new test folder shutil.move('res.filter.log', newpath) shutil.move('res.recode.vcf', newpath)
def run_vcf_to_filter1(vcf_in, seq_out): for i in range(len(list1)): print len(list1) # args = filter_final_list[4] args = list1[i] print args vcf_filter.run(args) print 'hello' print newpath[i] shutil.move('merged_chr1_10000' + name1, newpath[i]) shutil.move('merged_chr1_10000' + name1 + '.log', newpath[i]) #shutil.move('/home/staff/asukeshkall/Downloads/Test-3/Run/test1/merged_chr1_10000.recode.bcf','/home/staff/asukeshkall/Downloads/Test-3/') shutil.move( '/home/staff/asukeshkall/Downloads/Test-3/Run/' + folder + '/merged_chr1_10000.recode.bcf', '/home/staff/asukeshkall/Downloads/Test-3/')
def run_vcf_to_filter(vcf_in,seq_out): args = filter_final_list[4] #args = list1[i] vcf_filter.run(args)
def run_vcf_to_filter8(vcf_in, seq_out): args = [ 'merged_chr1_10000.vcf.gz', '--out-format', 'vcf.gz', '--out-prefix', 'merged_chr1_10000' ] vcf_filter.run(args)
def run_vcf_to_filter(vcf_in,seq_out): args = filter_final_list[12] vcf_filter.run(args)
def testFunc(lname,fn,np): vcf_filter.run(lname) self.assertTrue(os.path.isfile(file_names[fn])) self.assertTrue(os.path.isfile(file_names[fn]+'.log')) shutil.move(file_names[fn], newpath[np]) shutil.move(file_names[fn]+'.log', newpath[np])
def run_vcf_to_filter(vcf_in, seq_out): args = [vcf_in, '--out-format', 'bcf', '--out-prefix', 'merged_chr1_1000'] vcf_filter.run(args)
def run_vcf_to_filter(vcf_in,seq_out): args = [vcf_in] vcf_filter.run(args)