def run(self):
vcf_paths = self.param_required('allfiles2combine')
labels = self.param_required('alldatasets2combine')
vcf_utils = VcfUtils(
vcflist=vcf_paths,
bcftools_folder=self.param_required('bcftools_folder'),
gatk_folder=self.param_required('gatk_folder'),
tmp_dir=self.param('tmp_dir'))
ginterval = None
if self.param_is_defined('ginterval'):
ginterval = self.param('ginterval')
outfile = vcf_utils.combine(
labels=labels,
reference=self.param_required('reference'),
threads=self.param_required('threads'),
outprefix=self.param_required('outprefix'),
outdir=self.param_required('work_dir'),
compress=True,
genotypemergeoption='UNIQUIFY',
ginterval=ginterval,
options=['-env', '-sites_only', '--filteredAreUncalled'])
self.param('out_vcf', outfile)
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)
def run(self):
filepath = self.param_required('filepath')
self.warning('Analysing file: %s' % filepath)
basename = 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]
vcf_object = VcfUtils(vcf=filepath,
bgzip_folder=self.param('bgzip_folder'))
outprefix = "{0}/{1}".format(
work_dir,
basename + ".{0}".format(self.param_required('chr_types')))
outfile = vcf_object.rename_chros(
chr_types=self.param_required('chr_types'),
outfile=outprefix + ".vcf.gz")
self.param('vcf_f', outfile)
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 vcf_ambiguity():
'''
Returns a VcfUtils object that contains the REF or ALT column with some ambiguity codes
'''
vcf_file = pytest.config.getoption("--vcf_ambiguity")
vcf_object = VcfUtils(vcf=vcf_file)
return vcf_object
def run(self):
filepath = self.param_required('filepath')
newheader = self.param_required('newheader')
self.warning('Analysing file: %s' % filepath)
basename = 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]
vcf_object = VcfUtils(
vcf=filepath,
bcftools_folder=self.param_required('bcftools_folder'))
outprefix = "{0}/{1}".format(work_dir, basename)
outfile = ""
if self.param_is_defined('samplename'):
samplename = self.param('samplename')
try:
tfile = tempfile.NamedTemporaryFile(mode='w', dir='data/')
tfile.write(samplename + "\n")
tfile.flush()
outfile = vcf_object.reheader(
newheader=self.param_required('newheader'),
samplefile=tfile.name,
outprefix=outprefix)
finally:
# Automatically cleans up the file
tfile.close()
elif self.param_is_defined('samplefile'):
outfile = vcf_object.reheader(
newheader=self.param_required('newheader'),
samplefile=self.param('samplefile'),
outprefix=outprefix)
else:
outfile = vcf_object.reheader(
newheader=self.param_required('newheader'),
outprefix=outprefix)
self.param('vcf_f', outfile)
def vcf_object():
'''Returns an object'''
vcf_file = pytest.config.getoption("--vcf")
vcflist = pytest.config.getoption("--vcflist")
bcftools_folder = pytest.config.getoption("--bcftools_folder")
bgzip_folder = pytest.config.getoption("--bgzip_folder")
gatk_folder = pytest.config.getoption("--gatk_folder")
vcf_object=VcfUtils(vcf=vcf_file,bgzip_folder=bgzip_folder,vcflist=vcflist,bcftools_folder=bcftools_folder,
gatk_folder=gatk_folder)
return vcf_object
def test_change_chrnames_2ucsc():
'''
Test the method to change the style of the chrnames (from Ensembl to UCSC)
'''
vcf_object=VcfUtils(vcf='data/outdir/test.ensembl.vcf.gz',
bgzip_folder=pytest.config.getoption("--bgzip_folder"))
vcf_object.rename_chros(chr_types='ucsc', outfile='data/outdir/test.ucsc.vcf.gz')
vcf_object.rename_chros(chr_types='ucsc', outfile='data/outdir/test.ucsc.vcf', compress=False)
assert os.path.exists("data/outdir/test.ucsc.vcf.gz")
assert os.path.exists("data/outdir/test.ucsc.vcf")