Comments (2)
In the projects that I use dnaio.open
I think that works very well. Just like gzip.open
, lzma.open
etc. If fits very well with the style of python.
In practice, I always write SequenceRecord
objects that I read or modified. I do not really see a use for constructing FASTQ files on the fly. I mean, in that case "@" + name + "\n" + sequence + "\n+\n" + qualities + "\n"
and using a regular open function works much better anyway.
EDIT: Come to think of it, I only use dnaio.open
for reading. I use regular xopen
for writing and then use the fastq_bytes
method.
from dnaio.
Ok, writing the tutorial (#72) just now, I think I’m coming to the conclusion that adding the dnaio.
prefix in the rare cases it’s needed is acceptable. I believe what got me thinking about this was that I added type annotations to some functions in Cutadapt, and in those cases leaving out the dnaio.
prefix would be a bit nicer.
But let’s close this for now. Adding an alias for open
also increases complexity, which would be another reason against it.
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Related Issues (20)
- ResourceWarnings HOT 3
- FastqFormatError, while reading in chunks HOT 5
- Use a newline index for FastqIter HOT 10
- Add ubam support HOT 11
- check quality score integrity HOT 1
- Version 1.0 HOT 3
- Typing warnings from mypy HOT 7
- How to cite dnaio in a manuscript? HOT 2
- Extended BAM support HOT 4
- _Py_NegativeRefcount error HOT 7
- Remove BytesSequenceRecord HOT 2
- Does SequenceRecord need to support the buffer protocol? HOT 2
- SequenceRecord array class HOT 6
- Three-way is mate comparison HOT 2
- Switch single&paired API to single&multiple API. HOT 2
- Compilation error HOT 3
- Identifying bottlenecks HOT 4
- compresslevel and open_threads should be arguments in the dnaio.open interface
- Add better type hints for dnaio.open()
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