def test_convert_PL2GL(clean_tmp):
'''
Test the method change PL fields to GL in a VCF file
'''
vcf_object=VcfUtils(vcf='data/test.gatk.vcf.gz',
bcftools_folder=pytest.config.getoption("--bcftools_folder"))
vcf_object.convert_PL2GL(outfile='data/outdir/test.gatk.GL.vcf.gz',verbose=True)
assert os.path.exists("data/outdir/test.gatk.GL.vcf.gz")
def run(self):
filepath = self.param_required('filepath')
self.warning('Analysing file: %s' % filepath)
if not os.path.isdir(self.param_required('work_dir')):
os.makedirs(self.param_required('work_dir'))
threads = 1
if self.param_is_defined('threads'):
threads = self.param('threads')
outprefix = os.path.split(self.param_required('outprefix'))[1]
outfile = "{0}/{1}.GL.vcf.gz".format(self.param_required('work_dir'),
outprefix)
vcf_object = VcfUtils(
vcf=filepath,
bcftools_folder=self.param_required('bcftools_folder'))
vcf_file = vcf_object.convert_PL2GL(outfile,
threads=threads,
verbose=True)
self.param('out_vcf', vcf_file)