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graph-genome / component_segmentation

Read in ODGI Bin output and identify co-linear components
Apache License 2.0
3 stars 4 forks source link

I13 #17

Closed subwaystation closed 4 years ago

subwaystation commented 4 years ago

Moving segmentation.py take care of the imports. As matrixcomponent is seen as its own module, it is better to take our main python file out of the module it imports.

subwaystation commented 4 years ago

@josiahseaman @superjox @mandosoft could please someone verify this? For me, this did the trick.

josiahseaman commented 4 years ago

Thanks for looking into this. I'd like a second opinion. I can believe it fixes the problem. Though I doubt it's ideal. FluentDNA (one of my other projects) is pip installable and the main function and file is still inside the module. I import things in the same way, so it must be valid syntax in this situation. 

from FluentDNA.ParallelGenomeLayout import ParallelLayout
from FluentDNA.AnnotatedTrackLayout import  AnnotatedTrackLayout
from FluentDNA.Ideogram import Ideogram
from FluentDNA.HighlightedAnnotation import HighlightedAnnotation

This issue has me baffled. I suspect it's a quirk of the project setup somewhere.

Mark-Seaman commented 4 years ago

This change will work fine. The data directory must be moved to accommodate the existing command in the README.md file.