nawatts
commented
4 years ago Hi @imrannibmg,
It looks like this was happening for VCF files with a .gz extension, but not .bgz. This is because PyVCF constructs a GzipFile for file objects opened from a .gz file.
However, this is not necessary because convert_vcf_to_json.py handles compression outside of the PyVCF reader. The file object passed to the VCF Reader is created by gzip.open.
I tried converting VCF to JSON using the script. Resulted error.
Traceback (most recent call last): File "../convert_vcf_to_json.py", line 218, in
main()
File "../convert_vcf_to_json.py", line 213, in main
tag_fields=tag_fields,
File "../convert_vcf_to_json.py", line 69, in convert_vcf_to_json
reader = vcf.Reader(vcf_file)
File "/usr/local/lib/python3.7/site-packages/vcf/parser.py", line 300, in init
self._parse_metainfo()
File "/usr/local/lib/python3.7/site-packages/vcf/parser.py", line 317, in _parse_metainfo
line = next(self.reader)
File "/usr/local/lib/python3.7/site-packages/vcf/parser.py", line 280, in
self.reader = (line.strip() for line in self._reader if line.strip())
File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/codecs.py", line 645, in next
line = self.readline()
File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/codecs.py", line 558, in readline
data = self.read(readsize, firstline=True)
File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/codecs.py", line 498, in read
newdata = self.stream.read(size)
File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/gzip.py", line 276, in read
return self._buffer.read(size)
File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/gzip.py", line 463, in read
if not self._read_gzip_header():
File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/gzip.py", line 406, in _read_gzip_header
magic = self._fp.read(2)
File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/gzip.py", line 91, in read
self.file.read(size-self._length+read)
TypeError: can't concat str to bytes
Please help me out....