Compatibility of stitchr with Windows about stitchr HOT 5 CLOSED

Hello hello,

Ahh this is a Windows-specific thing, as I only really use stitchr on Linux and OSX. However I think I know what the problem is (Windows using back- instead of forward-slashes for paths).

Before I try to fix that, does stitchr -dd work for you? If so could you let me know what path it gives.

from stitchr.

Thank you for the prompt response. Unfortunately, stitchr -dd doesn't return anything.

I was also wondering if it would be possible to import stitchr and use it in a Python script or Jupyter Notebook. Thanks again!

from stitchr.

Fixed in e2d7895, v1.1.2, tested on Ubuntu/Mac OSX/Windows.

This also fixes importing stitchr to use in other scripts, which got broken in the conversion to a package. I wrote a quick synopsis of how to start doing so at https://jamieheather.github.io/stitchr/importing.html

The changes have been pushed to PyPI, so you should be able to upgrade or re-download with pip to get the changes.

from stitchr.

Awesome, thank you @JamieHeather!

I was wondering if it is possible to use stitchr for BCRs?

from stitchr.

You're very welcome - it was something I needed to get to sooner or later anyway!

So in theory yes it absolutely can be used for BCRs, which we demonstrate in the paper (and which has a section in the docs. However as everything is much more complicated in BCRs (and me not being a BCR expert) this isn't something that I'm able to fully support as I can with TCRs.

Generally speaking, what with greater levels of germline polymorphism and SHM I'd recommend using longer reads with the seamless option, and/or ensuring coverage of the relevant genes via the additional genes file. Either way when working with BCRs you might end up having to get under the hood a bit more. Happy to chat about specific use cases if the guidance in the docs isn't enough.

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