def detect_vcf_annotation(filepath):
"""Return the name of the annotation parser to be used on the given file
Called: In the importer and in the project wizard to display the detected
annotations.
:return: "vep", "snpeff", None
"""
if cm.is_gz_file(filepath):
# Open .gz files in binary mode (See #84)
device = open(filepath, "rb")
else:
device = open(filepath, "r")
std_reader = vcf.VCFReader(device)
# print(std_reader.metadata)
if "VEP" in std_reader.metadata:
if "CSQ" in std_reader.infos:
device.close()
return "vep"
if "SnpEffVersion" in std_reader.metadata:
if "ANN" in std_reader.infos:
device.close()
return "snpeff"
def __init__(self, filepath, *args, **kwargs):
self.count = 0
self.filepath = filepath
# Autodetection of string and filepaths
if not os.path.exists(self.filepath):
self.is_from_string = True
self.is_gz_file = False
else:
self.is_from_string = False
self.is_gz_file = cm.is_gz_file(filepath)
def get_total_file_size(self) -> int:
"""Compute file size int bytes"""
# FakeReader is used ?
if not self.device:
return 0
filename = self.device.name
if cm.is_gz_file(filename):
return cm.get_uncompressed_size(filename)
# Go to EOF and get position in bytes
size = self.device.seek(0, 2)
# Rewind the file
self.device.seek(0)
return size
def create_reader(filepath):
"""Context manager that wraps the given file and return an accurate reader
A detection of the file type is made as well as a detection of the
annotations format if required.
Filetypes and annotations parsers supported:
- vcf.gz: snpeff, vep
- vcf: snpeff, vep
- csv, tsv, txt: vep
"""
path = pathlib.Path(filepath)
LOGGER.debug(
"create_reader: PATH suffix %s, is_gz_file: %s",
path.suffixes,
cm.is_gz_file(filepath),
)
if ".vcf" in path.suffixes and ".gz" in path.suffixes:
annotation_detected = detect_vcf_annotation(filepath)
device = open(filepath, "rb")
reader = VcfReader(device, annotation_parser=annotation_detected)
yield reader
device.close()
return
if ".vcf" in path.suffixes:
annotation_detected = detect_vcf_annotation(filepath)
device = open(filepath, "r")
reader = VcfReader(device, annotation_parser=annotation_detected)
yield reader
device.close()
return
if {".tsv", ".csv", ".txt"} & set(path.suffixes):
device = open(filepath, "r")
reader = CsvReader(device)
yield reader
device.close()
return
raise Exception("create_reader:: Could not choose parser for this file.")