https://github.com/clinical-genomics/schug
All you need to know about genes, transcripts and exons
Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.8%) to scientific vocabulary
Repository
All you need to know about genes, transcripts and exons
Basic Info
- Host: GitHub
- Owner: Clinical-Genomics
- Language: Python
- Default Branch: main
- Homepage: https://clinical-genomics.github.io/schug/
- Size: 960 KB
Statistics
- Stars: 0
- Watchers: 5
- Forks: 0
- Open Issues: 7
- Releases: 17
Metadata Files
README.md
Schug
Schug :stew: is a service that gather data about genes, transcripts and exons from multiple sources and merge the information. There is a REST API with relevant endpoints.
Test the app using Docker
You can test Schug on your local computer using Docker. Make sure you have Docker installed and type the following commands in a terminal window:
git clone https://github.com/Clinical-Genomics/schug
cd schug
docker-compose up
Then the app endpoints should be listed available at the following address http://localhost:8000/docs
The command to stop the demo is docker-compose down.
Installation (development)
Make sure poetry is installed
git clone https://github.com/Clinical-Genomics/schug
cd schug
poetry install
schug serve --reload
Go to http://localhost:8000/docs and check out the API.
Ready-to-use endpoints
Once having set up an instance of Schug, you can use the following endpoints:
- /genes/ensembl_genes/
Downloads genes from Ensembl in text format. Specify a genome build by using the parameters 37 or 38.
Usage: curl -X 'GET' 'http://0.0.0.0:8000/genes/ensembl_genes/?build=38' > genes_GRCh38.txt
- /transcripts/ensembl_transcripts/
Downloads gene transcripts from Ensembl in text format. Specify a genome build by using the parameters 37 or 38.
Usage: curl -X 'GET' 'http://0.0.0.0:8000/transcripts/ensembl_transcripts/?build=38' > transcripts_GRCh38.txt
- /exons/ensembl_exons/
Downloads gene exons from Ensembl in text format. Specify a genome build by using the parameters 37 or 38.
Usage: curl -X 'GET' 'http://0.0.0.0:8000/exons/ensembl_exons/?build=38' > exons_GRCh38.txt
Issues While Downloading Genes, Transcripts, or Exons
You might encounter errors while downloading genes, transcripts, or exons, such as the following error:
httpx.RemoteProtocolError: peer closed connection without sending complete message body (incomplete chunked read)
This error often occurs when the external service prematurely closes the connection during data streaming. To address this issue, you can try increasing the max_tries parameter in your request, which otherwise defaults to 5. Increasing the number of retries can help handle intermittent network issues or temporary interruptions from the service.
Here’s an example of how to modify the request:
curl -X 'GET' 'http://0.0.0.0:8000/exons/ensembl_exons/?build=37&max_retries=10' > exons_GRCh37.txt`
What is left to do?
The basic structure is outlined and implemented, however there are many details left to implement before this can be used. Some of the basic endpoints are in place but these need to be extended according to the needs of the users. Also the gene information needs to be completed, this will be done in a similar fashion as in Scout.
Owner
- Name: Clinical Genomics
- Login: Clinical-Genomics
- Kind: organization
- Location: Stockholm, Sweden
- Website: https://clinical-genomics.github.io
- Repositories: 67
- Profile: https://github.com/Clinical-Genomics
GitHub Events
Total
- Create event: 35
- Release event: 9
- Issues event: 28
- Delete event: 24
- Issue comment event: 98
- Push event: 47
- Pull request review event: 6
- Pull request review comment event: 4
- Pull request event: 47
Last Year
- Create event: 35
- Release event: 9
- Issues event: 28
- Delete event: 24
- Issue comment event: 98
- Push event: 47
- Pull request review event: 6
- Pull request review comment event: 4
- Pull request event: 47
Committers
Last synced: 12 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Chiara Rasi | r****a@g****m | 88 |
| Chiara Rasi | r****a@g****m | 85 |
| Mei | 2****d | 17 |
| moonso | m****n@s****e | 7 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 43
- Total pull requests: 89
- Average time to close issues: about 1 month
- Average time to close pull requests: 10 days
- Total issue authors: 4
- Total pull request authors: 3
- Average comments per issue: 1.42
- Average comments per pull request: 1.89
- Merged pull requests: 78
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 16
- Pull requests: 46
- Average time to close issues: 5 days
- Average time to close pull requests: 1 day
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 2.56
- Average comments per pull request: 1.85
- Merged pull requests: 41
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- northwestwitch (34)
- Mropat (5)
- Jakob37 (1)
- henrikstranneheim (1)
Pull Request Authors
- northwestwitch (97)
- projectoriented (3)
- Vince-janv (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 629 last-month
- Total docker downloads: 255
- Total dependent packages: 1
- Total dependent repositories: 1
- Total versions: 17
- Total maintainers: 2
pypi.org: schug
Keep track of genes, transcripts and exons from different sources
- Documentation: https://schug.readthedocs.io/
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Latest release: 1.12.0
published about 1 year ago