https://github.com/brentp/geneimpacts
prioritize effects of variant annotations from VEP, SnpEff, et al.
Science Score: 33.0%
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Links to: biorxiv.org -
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1 of 11 committers (9.1%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (8.4%) to scientific vocabulary
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Repository
prioritize effects of variant annotations from VEP, SnpEff, et al.
Basic Info
Statistics
- Stars: 34
- Watchers: 3
- Forks: 16
- Open Issues: 6
- Releases: 0
Metadata Files
README.md
Given multiple snpEff or VEP or BCFTools consequence annotations for a single variant, get an orderable python object for each annotation.
This is to provide a consistent interface to different variant annotations such as from snpEff ANN field and the VEP CSQ field. and the BCFTools consequence field
This will be used in gemini but should also be of general utility.
Design
There is an effect base-class and then a sub-class for snpEff, one for VEP, and one for BCFT
Effect objects are orderable (via __le__ ) and should have an __eq__ method so that we can use functools.total_ordering to provide the other comparison operators.
Given 2 effects objects, a and b: a < b == True iff the severity of b is greater than a.
We will have a classmethod: `Effect.top_severity([eff1, ... effn]) that will return the single highest severity if that exists or a list of the ties for highest
Rules for severity:
Given 2 annotations, a and b a is more severe than b if:
- b is a pseudogene and a is not
- a is coding and b is not
- a has higher severity than b ( see below)
- polyphen, then sift
- ??? transcript length? (we dont have access to this).
severity
Severity is based on the impacts from VEP and the impacts from snpEff. We reduce from the 4 categories HIGH, MODERATE, LOW, MODIFIER to 3 by renaming MODERATE to MED and renaming MODIFIER to LOW.
Owner
- Name: Brent Pedersen
- Login: brentp
- Kind: user
- Location: Oregon, USA
- Twitter: brent_p
- Repositories: 220
- Profile: https://github.com/brentp
Doing genomics
GitHub Events
Total
- Watch event: 1
- Push event: 1
- Pull request review event: 2
- Pull request event: 3
- Fork event: 2
Last Year
- Watch event: 1
- Push event: 1
- Pull request review event: 2
- Pull request event: 3
- Fork event: 2
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Brent Pedersen (brentp) | b****e@g****m | 75 |
| roryk | r****r@g****m | 6 |
| chapmanb | c****b@5****m | 3 |
| Nilesh Patra | n****h@n****o | 2 |
| naumenko.sa | e****b@g****m | 1 |
| kew24 | k****a@v****g | 1 |
| Emmanuel Arias | e****u@y****m | 1 |
| Edward Betts | e****d@4****m | 1 |
| Bradford Powell | b****w@d****g | 1 |
| anastazie | a****d@g****m | 1 |
| Andrew Oler | a****r@n****v | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 9
- Total pull requests: 18
- Average time to close issues: 18 days
- Average time to close pull requests: about 17 hours
- Total issue authors: 8
- Total pull request authors: 12
- Average comments per issue: 1.22
- Average comments per pull request: 2.33
- Merged pull requests: 14
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: about 3 hours
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- brentp (2)
- slulla (1)
- bpow (1)
- naumenko-sa (1)
- arq5x (1)
- ilykos (1)
- oleraj (1)
- Luciagenetic (1)
- ToonRosseel (1)
Pull Request Authors
- chapmanb (5)
- roryk (3)
- eamanu (2)
- naumenko-sa (1)
- a113n (1)
- EdwardBetts (1)
- bpow (1)
- leifdreizler (1)
- wm75 (1)
- kew24 (1)
- oleraj (1)
- anastazie (1)
- nileshpatra (1)
Top Labels
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Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 1
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
spack.io: py-geneimpacts
Given multiple snpEff or VEP or BCFTools consequence annotations for a single variant, get an orderable python object for each annotation.
- Homepage: https://github.com/brentp/geneimpacts
- License: []
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Latest release: 0.3.7
published over 4 years ago