Comments (3)
We should try to keep bash scripting to a minimum. It's basically impossible to debug unless you're a bash wizard. Are you sure there isn't an equivalent function in python? How large is a large motif file and why can't pybedtools handle it?
from garnet.
This is pretty much all bedtools which has pretty good error reporting. pybedtools cannot handle it because some garnet files end up around 7gb, which requires generating individual garnet files for each motif, then concatenating them via bash anyways. Furthermore, command line is super fast (it took 12 min to generate that 7gb file).
from garnet.
Sounds reasonable to me.
from garnet.
Related Issues (20)
- Python version compatability HOT 2
- MotifMap has transfac IDs HOT 1
- MotifMap takes too long to load into RAM -- could we use a database? HOT 1
- Map Motifs to Gene Symbols HOT 2
- TF Regression Error HOT 9
- Include TF "targets" in output HOT 3
- check files exist HOT 1
- What does motif score mean? HOT 14
- Garnet file stuck loading HOT 1
- Bedtools can perform map_peaks function in ~1 min HOT 7
- Comparison: Garnet file generation HOT 1
- TF regression drop duplicates HOT 4
- `TF_regression` not working properly on server (or locally either) HOT 2
- Filter out unreasonable regressions HOT 2
- GarNet File has inconsistent naming convention for record: HOT 5
- mm9, mm10 garnet file construction notebooks HOT 3
- Window optional param HOT 3
- Idea for speed optimization.
- TODO: autofetch reference files HOT 1
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 garnet.