How to write a BGZF file with Biopython?
Hi everyone,
I've read the documentation for Bio.bgzf and I'm sufficiently confused by it.
To create an example bgzf file, I've tried the following. The write method internally uses _write_block which AFAICT adds a bgzf header. The close method flushes and adds the EOF marker.
from Bio import bgzf
header="hello\nworld\somestuff"
text="an\nexample\nbody"
test=bgzf.BgzfWriter("helloworld.bgzf")
test.write(header)
test.write(text)
test.close() # works fine
But when parsing, I'm getting a ValueError when parsing the file. zcat works just fine at the command line.
infile=bgzf.BgzfReader("helloworld.bgzf")
for values in bgzf.BgzfBlocks(infile):
print("Raw start %i, raw length %i; data start %i, data length %i" % values)
...
ValueError: A BGZF (e.g. a BAM file) block should start with b'\x1f\x8b\x08\x04', not 'hell'; handle.tell() now says 4
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