dnaio
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marcelm
Efficiently read and write sequencing data from Python
I added the ability for `dnaio.open` to open multiple files. I also added the `dnaio.open_multiple` API which iworks in case you want 1-tuples for 1 file. (I use this sort...
A while ago I watched some videos on optimization and having a look at generated assembly code. Since dnaio is a relatively straightforward project. I decided to have a go...
Currently I am working a lot with UMI data that is stored in a separate FASTQ file meaning I have 3 files now. I needed to filter those files on...
The discussion in #76 reminded me of an idea I had a while ago for possibly improving performance when dealing with many SequenceRecord objects: We could implement some kind of...
Currently dnaio uses a slightly unusual architecure where the first value of fastq_iter is a boolean, not a SequenceRecord. This determines whether all coming fastq headers are printed with two...
and also `Sequence.comment` and perhaps `Sequence.sep`. They could be lazily computed. Perhaps also add `.header` as an alias for `.name`? Should setting `.id` and `.comment` be supported? Convenient, but perhaps...
Hi, I have been working on the benchmarking and I am quite intrigued by fastp. The project is very similar to dnaio in terms of it API. Paired reading, writing,...
As discussed in https://github.com/marcelm/cutadapt/issues/757 adding BAM support to dnaio would have several advantages for cutadapt. The alternative is to defer to pysam instead, and keep dnaio at its basic level....
I am tring to use cutadapt to process my reads file, but I meet up with a problem ``` dnaio.exceptions.UnknownFileFormat: Could not determine whether file '' is FASTA or FASTQ....
Debian's linting tool "lintian" reports the below informational message in dnaio 1.2.2 (and possibly other versions): I: python3-dnaio: spelling-error-in-binary "allows to" "allows one to" [usr/lib/python3/dist-packages/dnaio/_core.cpython-312-x86_64-linux-gnu.so] This patch applies almost blindly...
