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Add gzip decompression from file #48

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Add gzip decompression from file #48

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10 changes: 10 additions & 0 deletions bioread/reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,8 @@
from __future__ import with_statement, division
import struct
import zlib
import gzip
import io as pyio
from contextlib import contextmanager

import numpy as np
Expand Down Expand Up @@ -80,6 +82,14 @@ def read(cls,

returns: reader.Reader.
"""

# decompresses gzip file into memory
if isinstance(fo, str) and fo.endswith('.gz'):
with gzip.open(fo, 'rb') as compressed_fo:
decompressed_data = compressed_fo.read()
fo = pyio.BytesIO(decompressed_data)


with open_or_yield(fo, 'rb') as io:
reader = cls(io)
reader._read_headers()
Expand Down