Comments (2)
Hi Wout!
Sorry for the long delay before my reply. Thank you very much for taking the lead on this one!
As I previously stated I think it remains important that pygor is supplied along with IGoR and I think it should still be included as a git submodule.
Here are the pros and cons I see about this separation:
Pros:
- use of PyPi
- smooth integration of the AIRR format (http://docs.airr-community.org/en/latest/packages/airr-python/overview.html)
Cons:
- some pieces of pygor extract information from IGoR's fileformats. This creates an interdependency between IGoR's and pygor releases. This is why I think including pygor in IGoR's releases would be good.
Development directions:
- cython interface between IGoR and pygor (this would probably solve the first con). This would also be very helpful to prototype codes before implementing in C++
- a small library to make summary plot from IGoR's outputs/distributions etc
- implement selection, clone frequency distributions generation etc (this would also be a good reason for having a cython interface, as a lot of these would not necessarily require coding in C for performance)
Tell me if you have other ideas I will append them to the list!
from igor.
Hi Quentin,
Sounds good! I have been taking some initiative on this one, since I needed to get started on doing some more of the master related work. Because of this I have cloned a version of pygor as one of my own repos (I made sure the your commit messages where carried over as well). You can find this version here: https://github.com/penuts7644/pygor and is installable via PyPI as well. I'm currently working on some refactoring work for the module (aka using more classes and separating the tools a bit more).
I agree with your pros and cons and am willing to implement these as time progresses. Just not right now because of my own priorities. Also I think that the cons can be solved (for now) by mentioning which version of pygor works with which version of IGoR in the readme file of pygor (or even IGoR).
Cython is really nice to implement for some speed improvements and I will also add some snippets for pythons own multiprocessing module (for example for pandas data frame manipulation tasks).
Have a great day!
Cheers, Wout
from igor.
Related Issues (20)
- File not found when IGoR is installed locally HOT 1
- Errors: python to parse the output results? HOT 2
- Model edge gene choice relations differ HOT 1
- Chain IGoR commands HOT 1
- Missing unknown subargument error for -output HOT 1
- Using the --coverage output subarg HOT 1
- using the --coverage error
- make new database HOT 2
- make check failures but make install worked HOT 1
- Segmentation Fault in -run_demo HOT 5
- Limiting IGoR's CPU usage HOT 1
- Install error HOT 2
- How to get everyone sequence clonotype ?
- the result file foo_indexed_CDR3s.csv HOT 1
- segfault with gcc > 7 HOT 2
- IGoR over-estimating TCR V deletions?
- installation from source
- All 0 output in infer and question about L_thresh
- Remove superfluous IMGT information in TCR beta model parms file
- Undefined reference error during compling
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from igor.