def run(self):
filepath = self.param_required('filepath')
self.warning('Analysing file: %s'% filepath)
file = os.path.split(filepath)[1]
work_dir = None
if self.param_is_defined('work_dir'):
work_dir = self.param_required('work_dir')
else:
work_dir = os.path.split(filepath)[0]
vcfNorm = VcfNormalize(vcf=filepath, vcflib_folder=self.param_required('vcflib_folder'),
bgzip_folder=self.param_required('bgzip_folder'))
downstream_pipe = None
if self.param_is_defined('downstream_pipe'):
downstream_pipe = self.param('downstream_pipe')
vcf_file = ""
if self.param_is_defined('compress'):
vcf_file = vcfNorm.run_vcfallelicprimitives(outprefix=file,
compress=True,
downstream_pipe=downstream_pipe,
outdir=work_dir)
else:
vcf_file = vcfNorm.run_vcfallelicprimitives(outprefix=file,
compress=False,
downstream_pipe=downstream_pipe,
outdir=work_dir)
self.param('out_vcf', vcf_file)
def run(self):
filepath = self.param_required('filepath')
self.warning('Analysing file: %s' % filepath)
file = os.path.split(filepath)[1]
work_dir = None
if self.param_is_defined('work_dir'):
if not os.path.isdir(self.param('work_dir')):
os.makedirs(self.param('work_dir'))
work_dir = self.param('work_dir')
else:
work_dir = os.path.split(filepath)[0]
outprefix = "{0}/{1}".format(self.param('work_dir'), file)
vcfNorm = VcfNormalize(
vcf=filepath,
bcftools_folder=self.param_required('bcftools_folder'))
vcf_file = vcfNorm.run_bcftoolsnorm(
outprefix=outprefix,
reference=self.param_required('reference'),
multiallelics=self.param('multiallelics'),
type=self.param('type'))
self.param('out_vcf', vcf_file)
def run(self):
filepath = self.param_required('filepath')
self.warning('Analysing file: %s' % filepath)
file = os.path.split(filepath)[1]
work_dir = None
if self.param_is_defined('work_dir'):
work_dir = self.param_required('work_dir')
else:
work_dir = os.path.split(filepath)[0]
vcfNorm = VcfNormalize(
vcf=filepath,
vt_folder=self.param_required('vt_folder'),
bgzip_folder=self.param_required('bgzip_folder'))
vcf_file = ""
if self.param_is_defined('compress'):
vcf_file = vcfNorm.run_vtnormalize(
outprefix=file,
reference=self.param_required('reference'),
compress=True,
outdir=work_dir)
else:
vcf_file = vcfNorm.run_vtnormalize(
outprefix=file,
reference=self.param_required('reference'),
compress=False,
outdir=work_dir)
self.param('vcf_file', vcf_file)
def run(self):
filepath = self.param_required('filepath')
self.warning('Analysing file: %s' % filepath)
file = os.path.split(filepath)[1]
work_dir = None
if self.param_is_defined('work_dir'):
work_dir = self.param_required('work_dir')
else:
work_dir = os.path.split(filepath)[0]
vcfNorm = VcfNormalize(
vcf=filepath,
gatk_folder=self.param_required('gatk_folder'),
bgzip_folder=self.param_required('bgzip_folder'))
vcf_file = ""
if self.param_is_defined('compress'):
compress = None
if self.param('compress') == 'True':
compress = True
elif self.param('compress') == 'False':
compress = False
else:
raise Exception('compress parameter is not valid: {0}'.format(
self.param('compress')))
vcf_file = vcfNorm.run_gatk_VariantsToAllelicPrimitives(
outprefix=file,
reference=self.param_required('reference'),
outdir=work_dir,
compress=compress)
else:
vcf_file = vcfNorm.run_gatk_VariantsToAllelicPrimitives(
outprefix=file,
reference=self.param_required('reference'),
outdir=work_dir)
self.param('vcf_file', vcf_file)
def vcf_object():
'''Returns an object'''
vcf_file = pytest.config.getoption("--vcf")
bcftools_folder = pytest.config.getoption("--bcftools_folder")
bgzip_folder = pytest.config.getoption("--bgzip_folder")
vcflib_folder = pytest.config.getoption("--vcflib_folder")
vt_folder = pytest.config.getoption("--vt_folder")
gatk_folder = pytest.config.getoption("--gatk_folder")
vcf_object = VcfNormalize(vcf=vcf_file,
bgzip_folder=bgzip_folder,
vcflib_folder=vcflib_folder,
vt_folder=vt_folder,
bcftools_folder=bcftools_folder,
gatk_folder=gatk_folder)
return vcf_object