def get_vcf(self,
processed_dir: str = "",
real_path: str = "") \
-> [str]:
'''Get a list of vcf files.
'''
if real_path:
vcfs = [real_path]
else:
if 'documents' not in self._js:
return []
# vcfs are saved inside documents and marked by is_vcf
vcfs = [
d['document_name'] for d in self._js['documents']
if d and d['is_vcf']
]
# return empty if no vcfs present
if not vcfs:
return []
case_id = self.get_case_id()
if os.path.exists(vcfs[0]):
vcf_path = vcfs[0]
LOGGER.info("Case %s, VCF file %s is found.", case_id, vcfs[0])
destination_vcf = os.path.join(processed_dir, case_id + ".vcf.gz")
else:
vcf_dir = os.path.join(self._base_dir, "vcfs")
raw_vcfs = list(os.listdir(vcf_dir))
# convert and save vcfs to specified location if not already present
processed_vcfs = [
f.strip(".vcf.gz") for f in os.listdir(processed_dir)
]
destination_vcf = os.path.join(processed_dir, case_id + ".vcf.gz")
case_vcfs = [v for v in raw_vcfs if case_id in v]
if not case_vcfs:
LOGGER.info("Case %s, VCF file %s could not be found.",
case_id, vcfs[0])
return []
vcf = case_vcfs[0]
vcf_path = os.path.join(vcf_dir, vcf)
move_vcf(vcf_path, destination_vcf)
return [destination_vcf]
def get_vcf(self, processed_dir: str = "data/PEDIA/vcfs/original") \
-> [str]:
'''Get a list of vcf files.
'''
# vcfs are saved inside documents and marked by is_vcf
vcfs = [
d['document_name'] for d in self._js['documents']
if d and d['is_vcf']
]
# return empty if no vcfs present
if not vcfs:
return []
vcf_dir = os.path.join(self._base_dir, "vcfs")
raw_vcfs = list(os.listdir(vcf_dir))
# convert and save vcfs to specified location if not already present
processed_vcfs = [
f.strip(".vcf.gz") for f in os.listdir(processed_dir)
]
case_id = self.get_case_id()
destination_vcf = os.path.join(processed_dir, case_id + ".vcf.gz")
if case_id not in processed_vcfs:
case_vcfs = [v for v in raw_vcfs if case_id in v]
if not case_vcfs:
LOGGER.info("Case %s, VCF file %s could not be found.",
case_id, vcfs[0])
return []
vcf = case_vcfs[0]
vcf_path = os.path.join(vcf_dir, vcf)
kind = filetype.guess(vcf_path)
# get mimetype
mime = kind.mime if kind is not None else "text"
move_vcf(vcf_path, destination_vcf, mime)
return [destination_vcf]
def dump_vcf(self, path: str, recreate: bool = False) -> None:
'''Dumps vcf file to given path. Initializes vcf generation if none has yet been created.
Created vcf is saved to self.vcf.
'''
if hasattr(self, 'vcf') and not recreate:
if isinstance(self.vcf, str):
LOGGER.debug(
"VCF generation for case %s failed. Error message:%s", self.case_id, self.vcf)
else:
outputpath = os.path.join(path, self.case_id + '.vcf')
# add header to vcf
with open(outputpath, 'w') as outfile:
outfile.write(
'##fileformat=VCFv4.1\n##INFO=<ID=HGVS,Number=1,Type=String,Description="HGVS-Code">\n##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n')
outfile.write(
'##contig=<ID=1,assembly=b37,length=249250621>\n')
outfile.write(
'##contig=<ID=2,assembly=b37,length=243199373>\n')
outfile.write(
'##contig=<ID=3,assembly=b37,length=198022430>\n')
outfile.write(
'##contig=<ID=4,assembly=b37,length=191154276>\n')
outfile.write(
'##contig=<ID=5,assembly=b37,length=180915260>\n')
outfile.write(
'##contig=<ID=6,assembly=b37,length=171115067>\n')
outfile.write(
'##contig=<ID=7,assembly=b37,length=159138663>\n')
outfile.write(
'##contig=<ID=8,assembly=b37,length=146364022>\n')
outfile.write(
'##contig=<ID=9,assembly=b37,length=141213431>\n')
outfile.write(
'##contig=<ID=10,assembly=b37,length=135534747>\n')
outfile.write(
'##contig=<ID=11,assembly=b37,length=135006516>\n')
outfile.write(
'##contig=<ID=12,assembly=b37,length=133851895>\n')
outfile.write(
'##contig=<ID=13,assembly=b37,length=115169878>\n')
outfile.write(
'##contig=<ID=14,assembly=b37,length=107349540>\n')
outfile.write(
'##contig=<ID=15,assembly=b37,length=102531392>\n')
outfile.write(
'##contig=<ID=16,assembly=b37,length=90354753>\n')
outfile.write(
'##contig=<ID=17,assembly=b37,length=81195210>\n')
outfile.write(
'##contig=<ID=18,assembly=b37,length=78077248>\n')
outfile.write(
'##contig=<ID=19,assembly=b37,length=59128983>\n')
outfile.write(
'##contig=<ID=20,assembly=b37,length=63025520>\n')
outfile.write(
'##contig=<ID=21,assembly=b37,length=48129895>\n')
outfile.write(
'##contig=<ID=22,assembly=b37,length=51304566>\n')
outfile.write(
'##contig=<ID=X,assembly=b37,length=155270560>\n')
outfile.write(
'##contig=<ID=Y,assembly=b37,length=59373566>\n')
self.vcf.to_csv(outputpath, mode='a', sep='\t', index=False,
header=True, quoting=csv.QUOTE_NONE)
move_vcf(outputpath, outputpath + '.gz', 'text')
os.remove(outputpath)
# catches cases without genomic entries
elif not self.hgvs_models or not self.get_variants():
LOGGER.debug('VCF generation for case %s not possible, Error message: No variants',self.case_id)
else:
LOGGER.debug("Generating VCF for case %s", self.case_id)
self.vcf = self.create_vcf(path)
self.dump_vcf(path)
