Seq – A Language for Bioinformatics

Re:Seq – A Language for Bioinformatics by chromatin on Tuesday January 21, 2020 @12:42PM (#22109231)

Fascinating, but there exist already htslib [0] bindings for Python (and many other languages). htslib truly is the standard library with respect to high-throughput sequencing data file access, and with high level bindings, we can already write something like:

``` for seq in bamfile: print(seq.pos) ``` or whatever.

[0] https://github.com/samtools/htslib

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Re:Seq – A Language for Bioinformatics by snackematician on Tuesday January 21, 2020 @01:27PM (#22109815)

To expand on this -- I believe pysam [0] is the official htslib interface for Python.

It's quite good. In addition to providing Python bindings, it also provides extra functionality from within Cython, if you need additional features/speed but don't want to drop all the way down to C.

[0] https://pysam.readthedocs.io/en/latest/

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Re:Seq – A Language for Bioinformatics by mbreese on Tuesday January 21, 2020 @04:28PM (#22111803)

Is the pysam API more stable now? Years ago, I had to stop using it because the API has changed between versions too much.

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