Conversion to Python3

[luidale]

I converted Pybam to Python3. It is not fully functional (only dynamic parsing is functional).
It is currently available https://github.com/luidale/pybam.

Would it be reasonable to incorporate/add to original pybam repository? Update to fully functional?

[JontySinai]

I second this. @JohnLonginotto any plans to update the codebase to Python3?

Great work on pybam - excellent and simple API - but would really appreciate if it could work in Python3.

[JohnLonginotto]

wow, thanks guys. I really appreciate the interest and i'm sorry i wasn't maintaining this project better over the past year.

My interest in pybam (and genomics in general) declined quite rapidly after I discovered some serious errors in the BAM format (mainly, that most BAM files aren't actually standard compliant in a really big, totally undiscussed way, related to how mate alignments get paired up together). This is an unfixable bug in the format, and really a totally new format needs to be made from scratch that stores sequenced fragments.

Unfortunately, we all know that is never going to happen, the Network Effect being what it is. As such, I cannot recommend anyone uses the BAM format, and by extension, pybam. I feel like, by creating pybam, i have supported the status-quo usage of the BAM format over newer ideas.

However I'm sure there are plenty of people who just want to copy-paste a pure python BAM file reader into their script, and if someone wants to continue that going forwards, i'll happily convert the static-parser part of pybam to Py3, and hand-off responsibility for the code going forward. I really believe the static compiler is important, as it helps combat the non-deterministic nature of a lot of bioinformatic analyses. I'll do this over the coming days, with a release before next weekend. Now is a particularly good time actually, because the PyPy project (which this pure-python BAM reader benefits from dramatically) now supports Py3 very well.

All the best!

[GEOFBOT]

most BAM files aren't actually standard compliant in a really big, totally undiscussed way, related to how mate alignments get paired up together

Hey, I wanted to write some BAM parsing-related utilities as a personal exercise, and found this project. Could you clarify how most BAM files aren't standard compliant in practice? Cheers!

[shubhamLondhe]

pip install pybam not working

[palao]

@JohnLonginotto,
Thanks a lot for this package.

I read your comments in this issue, but I still need to process bam files with Python.
I see three options:

1. are you planning to release a Python3 version of pybam?
2. should I (or someone else) make it happen and create a pull request?
3. do you prefer that we fork the project?

Let me know, if possible.

Other options rely on wrappers on top of other dependencies (pysam, samtools) and that makes the installation process of our package more complex.