AnnotSV implementation in Python

[lgmgeo]

Hi users,

I'm wondering if anyone might be interested to implement AnnotSV in Python?
Then our users community could easily contribute towards it:

• Bugs could be tackled efficiently
• New ideas could be investigated faster

I look forward to the possibility of working together,
Hope someone might be interested in this nice and collaborative work.

Véronique
PS: The AnnotSV Source code is and will remain available under the GNU GPL licence

[serge2016]

I am interested in it, but I think I can only test it.. I don't feel myself free enough in python..

[lgmgeo]

Hi Sergey,

Thanks for considering to test AnnotSV in Python. I keep that in mind.

Currently, new ideas/features to investigate in AnnotSV are piling up... and I can't achieve everything ;o(
So a Python implementation really makes sense for me, to encourage participation by everyone.
Help from someone experienced with Python is welcome.

Best,
Véronique

[cangfengzhe]

AnnotSV is the best software I have ever used for SV annotation.
If AnnotSV implementation in Python, I will be interested in this nice and collaborative work.

[lgmgeo]

Hi LiPidong,
Thank you, it's nice to hear that you have found AnnotSV useful.
Can you contact me by email at [email protected]?
Best,
Véronique

[alfortega]

Hi!

This is an old thread, but I would like to add a question/suggestion here. I have recently been exploring various bioinformatics tools for CNV annotation, and it got me thinking about the possibility of having AnnotSV as an R package. I am reaching out to inquire if you have considered implementing AnnotSV as an R package.

I'm unsure whether it makes sense, considering the current AnnotSV tool works quite efficiently. Nevertheless, the R environment is widely used among researchers and provides a robust ecosystem for data analysis and visualization. AnnotSV as an R package could enhance its accessibility and usability within the R community and integrate AnnotSV in R-based analysis pipelines along other popular R packages, allowing seamless analysis workflows.

If you have not yet explored the idea of an R package for AnnotSV, I would be more than happy to offer my assistance. I have yet to gain experience developing R packages, but I'm proficient in R coding. I could contribute to the development efforts by adapting the existing codebase to R, creating appropriate documentation, or smoothly integrating existing R tools and data structures.

I appreciate the valuable work you have put into developing AnnotSV.
Best regards,
Alfredo Ortega, PhD.
University of Helsinki

[lgmgeo]

Hi Alfredo,

Thanks for your interest in AnnotSV ;o)
Actually, I never considered implementing AnnotSV as an R package and you are the first to submit the idea.

Unfortunately, I'm not proficient in R coding. And, as you can see with this old thread, I'm running out of time to implement AnnotSV in Python. So I won't be able to invest time in this R project.
However, I am open and interested in any new collaboration around AnnotSV. I love open science!
So feel free to adapt the existing codebase to R and create appropriate documentation. It will benefit the community.

However, keep in mind that this is a long-term investment, and that the R version should be updated in parallel with the Tcl version.

Best,
Véronique