def run(self):
self.warning('Analysing file: %s' % self.param_required('filepath'))
filepath = self.param_required('filepath')
vcf = BCFTools(vcf=filepath,
bcftools_folder=self.param_required('bcftools_folder'))
outprefix = ""
if self.param_is_defined('work_dir'):
file = os.path.split(filepath)[1]
outprefix = self.param('work_dir') + "/" + file
else:
outprefix = filepath
uncalled = None
if self.param_is_defined('uncalled'):
uncalled = self.param('uncalled')
if uncalled != 'include' and uncalled != 'exclude':
raise Exception(
"Valid 'uncalled' values are 'include'/'exclude'")
threads = 1
if self.param_is_defined('threads'):
threads = self.param('threads')
outfile = vcf.select_variants(outprefix=outprefix,
threads=threads,
uncalled=uncalled)
self.param('out_vcf', outfile)
def run(self):
self.warning('Analysing file: %s'% self.param_required('filepath'))
vcf = BCFTools(vcf=self.param_required('filepath'),
bcftools_folder=self.param_required('bcftools_folder'))
outvcf = vcf.filter(name=self.param_required('filter_name'),
expression=self.param_required('filter_expression'))
self.param('out_vcf', outvcf)
def run(self):
self.warning('Analysing file: %s' % self.param_required('filepath'))
filepath = self.param_required('filepath')
vcf = BCFTools(vcf=filepath,
bcftools_folder=self.param_required('bcftools_folder'))
outprefix = ""
if self.param_is_defined('work_dir'):
file = os.path.split(filepath)[1]
outprefix = self.param('work_dir') + "/" + file
else:
outprefix = filepath
biallelic = None
if self.param_is_defined('biallelic'):
if self.param('biallelic') == "True":
biallelic = True
elif self.param('biallelic') == "False":
biallelic = False
else:
raise Exception(
"Error. biallelic option should be True or False")
compress = True
if self.param_is_defined('compress'):
if self.param('compress') == "True":
compress = True
elif self.param('compress') == "False":
compress = False
else:
raise Exception(
"Error. compress option should be True or False")
outfile = vcf.filter_by_variant_type(
v_type=self.param_required('type'),
outprefix=outprefix,
biallelic=biallelic,
compress=compress)
self.param('out_vcf', outfile)
def run(self):
self.warning('Split file: %s' % self.param_required('filepath'))
ifile = self.param_required('filepath')
file = os.path.split(ifile)[1]
outdir = self.param_required('work_dir')
faix = self.param_required('faix')
verbose = None
if self.param_is_defined('verbose'):
verbose = self.__str_to_bool(self.param('verbose'))
filt_string = None
if self.param_is_defined('filt_string'):
filt_string = self.param('filt_string')
bcftools_o = BCFTools(vcf=ifile,
bcftools_folder=self.param('bcftools_folder'))
files = []
ix = 1
for line in open(faix):
if line.startswith("\n"):
continue
chrom = line.split('\t')[0]
self.warning('Splitting %s' % chrom)
chr_folder = outdir + "/" + chrom
if not os.path.isdir(chr_folder):
os.mkdir(chr_folder)
vcffile = bcftools_o.subset_vcf(region=chrom,
outprefix=file,
outdir=chr_folder,
create_index=True,
apply_filters=filt_string,
threads=self.param('threads'),
action='include',
verbose=verbose)
files.append({'chr': vcffile, 'ix': ix, 'chromname': chrom})
ix += 1
self.param('files', files)
def run(self):
filepath = self.param('filepath')
file = os.path.split(filepath)[1]
work_dir = os.path.split(filepath)[0]
if self.param_is_defined('work_dir'):
work_dir = self.param('work_dir')
self.warning('Analysing file: %s' % filepath)
if self.param('verbose') == "True":
print("Workdir is %s" % work_dir)
vcfFilter = BCFTools(vcf=filepath,
bcftools_folder=self.param('bcftools_folder'))
vcffile = vcfFilter.subset_vcf(bed=self.param_required('bed'),
outprefix=file + ".exc.vcf.gz",
outdir=work_dir,
create_index=True,
threads=self.param('threads'),
action=self.param('action'))
self.param('subset_file', vcffile)
self.param('subset_file_ix', vcffile + '.tbi')
def vcf_object():
'''Returns an object'''
vcf_file = pytest.config.getoption("--vcf")
bcftools_folder = pytest.config.getoption("--bcftools_folder")
vcf_object = BCFTools(vcf=vcf_file, bcftools_folder=bcftools_folder)
return vcf_object