module 'bgzip' has no attribute 'Reader'

[sandyplus]

Dear xbrianh,
I tried to use bgzip to read or write bgzip files, but I got this error:
module 'bgzip' has no attribute 'Reader'

my testing code:

import bgzip

with open("input.recode.vcf.gz",'rb') as raw:
     with bgzip.Reader(raw) as fh:
         for line in fh:
             line = line.strip()
             if line.startswith("##CHROM"):
                 print(line)

Did I miss somthing?
Best regards,
sandy

[xbrianh]

Hi Sandy,

Please use try this instead:

import bgzip

with open("input.recode.vcf.gz",'rb') as raw:
     with bgzip.BGZipReader(raw) as fh:
         for line in fh:
             line = line.strip()
             if line.startswith("##CHROM"):
                 print(line)

• Brian

[sandyplus]

Dear Brian,

I tried, but failed.
I still got error:

In [3]:
   ...: #decode bytes lines if your read lines from gzip file
   ...: def decode_line(line):
   ...:     if type(line) == bytes:
   ...:         line = line.decode('utf-8')
   ...:     return line
   ...:

In [4]: with open("test.Qrob_H2.3_Sc0000249.Ql_vs_Qm.mis0.7.mac.recode.vcf.gz",'r') as fh:
   ...:     with bgzip.BGZipReader(fh) as infile:
   ...:         for line in infile:
   ...:             line = line.strip()
   ...:             line = decode_line(line)
   ...:             if line.startswith("#CHROM"):
   ...:                 print(line)
   ...:
---------------------------------------------------------------------------
UnicodeDecodeError                        Traceback (most recent call last)
<ipython-input-4-1e14e3c681f1> in <module>
      1 with open("test.Qrob_H2.3_Sc0000249.Ql_vs_Qm.mis0.7.mac.recode.vcf.gz",'r') as fh:
      2     with bgzip.BGZipReader(fh) as infile:
----> 3         for line in infile:
      4             line = line.strip()
      5             line = decode_line(line)

/mnt/Data_disk/biosoft/anaconda3/envs/my_python3/lib/python3.7/site-packages/bgzip/__init__.py in read(self, size)
     34                 del self._buffer[:self._pos]
     35                 self._pos = 0
---> 36             self._input_data += self.fileobj.read(self.raw_read_chunk_size)
     37             if not self._input_data:
     38                 break

/mnt/Data_disk/biosoft/anaconda3/envs/my_python3/lib/python3.7/codecs.py in decode(self, input, final)
    320         # decode input (taking the buffer into account)
    321         data = self.buffer + input
--> 322         (result, consumed) = self._buffer_decode(data, self.errors, final)
    323         # keep undecoded input until the next call
    324         self.buffer = data[consumed:]

UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

Any suggestions?
Best regards,
Sandy

[xbrianh]

Hi Sandy,

One suggestion :)

The gzipped file should be opened in binary mode:

with open("test.Qrob_H2.3_Sc0000249.Ql_vs_Qm.mis0.7.mac.recode.vcf.gz", 'rb') as fh:

Note the "rb" open mode.

[sandyplus]

Dear Brian,

still not working

In [4]: with open("input_vcf/Qrob_H2.3_Sc0000249_191.filter.reheader.mac.recode.vcf.gz",'rb') as raw:
   ...:     with bgzip.BGZipReader(raw) as fh:
   ...:         for line in fh:
   ...:             line = line.strip()
   ...:             if line.startswith("#CHROM"):
   ...:                 print(line)
   ...:
---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-4-05e83853420c> in <module>
      1 with open("input_vcf/Qrob_H2.3_Sc0000249_191.filter.reheader.mac.recode.vcf.gz",'rb') as raw:
      2     with bgzip.BGZipReader(raw) as fh:
----> 3         for line in fh:
      4             line = line.strip()
      5             if line.startswith("#CHROM"):

OSError: read() should have returned a bytes object, not 'bytearray'

[SilasK]

It would be great if yu modify the pip page form Reader to BGZipReader.

[xbrianh]

@SilasK done, thanks!

[nbbarrientos]

Dear Brian,

still not working

In [4]: with open("input_vcf/Qrob_H2.3_Sc0000249_191.filter.reheader.mac.recode.vcf.gz",'rb') as raw:
   ...:     with bgzip.BGZipReader(raw) as fh:
   ...:         for line in fh:
   ...:             line = line.strip()
   ...:             if line.startswith("#CHROM"):
   ...:                 print(line)
   ...:
---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-4-05e83853420c> in <module>
      1 with open("input_vcf/Qrob_H2.3_Sc0000249_191.filter.reheader.mac.recode.vcf.gz",'rb') as raw:
      2     with bgzip.BGZipReader(raw) as fh:
----> 3         for line in fh:
      4             line = line.strip()
      5             if line.startswith("#CHROM"):

OSError: read() should have returned a bytes object, not 'bytearray'

Hello, were you able to figure out this issue? I encountered it too but I wasn't sure how to solve it. Thanks

[xbrianh]

@nbbarrientos @sandyplus

Since textual content is expected for a VCF file, the best solution is to use io.TextIOWrapper:

import io

with open("input_vcf/Qrob_H2.3_Sc0000249_191.filter.reheader.mac.recode.vcf.gz", 'rb') as raw:             
    with bgzip.BGZipReader(raw) as bgzip_fh:
        with io.TextIOWrapper(bgzip_fh, "utf-8") as fh:
            for line in fh:
                ...

[xbrianh]

In the next release of bgzip, the following will work:

with open("my_bgzip_file.bz", 'rb') as raw:             
    with bgzip.BGZipReader(raw) as fh:
        for line in fh:
            ...

However, note that line is bytes, not str. To get a string you must either use io.TextIOWrapper as above, or line.decode("utf-8").

[nbbarrientos]

In the next release of bgzip, the following will work:

with open("my_bgzip_file.bz", 'rb') as raw:             
    with bgzip.BGZipReader(raw) as fh:
        for line in fh:
            ...

However, note that line is bytes, not str. To get a string you must either use io.TextIOWrapper as above, or line.decode("utf-8").

Awesome, thank you very much. This is very helpful!!