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)
