Ancient DNA mode: Add pyDamage results to bin_summary.tsv
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- #835 by @jfy133 — closed without merging
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Description
Description of feature
Currently the pyDamage results are on a contig level, but it would be good to get a summary statistic in bin_summary.tsv so a user can evaluate which bins contain contigs with aDNA damage, when running with ancient DNA mode.
This will likely require parsing the pydamage results file, parsing ??? to get contigs in each bin, sorting the pydamage results per-contig results into the bins, making the median average across all columns (@alexhbnr 's approach), then adding this to the bin_summary table.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating where bin_summary.tsv is generated and where ancient DNA mode handles pyDamage results. Trace how contigs are mapped to bins, then determine how the per-contig results should be aggregated. Done means bin_summary.tsv includes the requested pyDamage summary for bins when ancient DNA mode is enabled.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100