LewisLabUCSD / LewisLabUCSD/Mito_Trace

Add the MT clone map that can contain multiple mutants in lineages

Open
#6 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

todo
Dominant language
Jupyter Notebook
Stars
0
Forks
0
No merged PRs in 30d

Description

Add the MT clone map that can contain multiple mutants in lineages

https://github.com/LewisLabUCSD/Mito_Trace/blob/f69c7a3e1612fbb847d3d4ecb280b16d01969b6d/src/simulations/pipeline.py#L179

            for i in range(1,num_clones+1):
                self.clone_mt_dict[i] = i
        # TODO Add the MT clone map that can contain multiple mutants in lineages


        # If there is a heteroplasmy table in params, it is list of mutant heteroplasmy AFs.

4f38161d12f40a52e61566e717a72784ab4b2b7d

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Read src/simulations/pipeline.py around line 179, including the existing clone_mt_dict initialization and the heteroplasmy-table note. Determine the intended representation for multiple mitochondrial mutants within lineages; the work is done when the clone map supports that case in the simulation pipeline.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.