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Open Source Science

https://github.com/bihealth/dotty

cdot-based transcript projections

https://github.com/bihealth/dotty

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

cdot-based transcript projections

Basic Info
  • Host: GitHub
  • Owner: bihealth
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 540 KB
Statistics
  • Stars: 0
  • Watchers: 4
  • Forks: 0
  • Open Issues: 4
  • Releases: 8
Created over 2 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog Contributing License Authors

README.md

CI codecov

dotty - cdot-based position projection

What can it do?

Run it the background, e.g., from main as

$ DATA_DIR=$PWD/data \ pipenv run uvicorn dotty.main:app --host 0.0.0.0 --port 8080 --reload

Then, resolve c./n./g. variants to SPDI-like variants

$ curl 'http://127.0.0.1:8080/api/v1/to-spdi?q=NM_000059.3:c.274G%3EA' 2>/dev/null | jq . { "spdi": { "assembly": "GRCh38", "contig": "13", "pos": 32319283, "reference_deleted": "C", "alternate_inserted": "A" } }

Obtaining Data

datasets is the NCBI datasets tool.

``` $ mkdir -p data $ cd data

$ wget \ https://github.com/SACGF/cdot/releases/download/v0.2.21/cdot-0.2.21.ensembl.grch37.json.gz \ https://github.com/SACGF/cdot/releases/download/v0.2.21/cdot-0.2.21.ensembl.grch38.json.gz \ https://github.com/SACGF/cdot/releases/download/v0.2.21/cdot-0.2.21.refseq.grch37.json.gz \ https://github.com/SACGF/cdot/releases/download/v0.2.21/cdot-0.2.21.refseq.grch38.json.gz

$ download genome accession GCF000001405.25 --filename GRCh37.zip $ download genome accession GCF000001405.40 --filename GRCh38.zip $ unzip GRCh37.zip $ unzip GRCh38.zip $ seqrepo --root-directory $PWD load --namespace ncbi --instance-name seqrepo ncbidataset/data/GCF000001405./.fna $ rm -rf GRCh3?.zip ncbi_dataset ```

Dump OpenAPI Schema

```

python -m dotty.main > openapi.yaml

```

Owner

  • Name: Berlin Institute of Health
  • Login: bihealth
  • Kind: organization

BIH Core Unit Bioinformatics & BIH HPC IT

GitHub Events

Total
  • Delete event: 46
  • Issue comment event: 2
  • Push event: 41
  • Pull request event: 93
  • Create event: 42
Last Year
  • Delete event: 46
  • Issue comment event: 2
  • Push event: 41
  • Pull request event: 93
  • Create event: 42

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 5
  • Total pull requests: 93
  • Average time to close issues: about 24 hours
  • Average time to close pull requests: 1 day
  • Total issue authors: 2
  • Total pull request authors: 4
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.31
  • Merged pull requests: 83
  • Bot issues: 0
  • Bot pull requests: 75
Past Year
  • Issues: 0
  • Pull requests: 29
  • Average time to close issues: N/A
  • Average time to close pull requests: about 7 hours
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.03
  • Merged pull requests: 24
  • Bot issues: 0
  • Bot pull requests: 29
View more stats
Top Authors
Issue Authors
  • holtgrewe (3)
  • gromdimon (3)
  • dependabot[bot] (2)
Pull Request Authors
  • dependabot[bot] (135)
  • varfish-bot (8)
  • holtgrewe (8)
  • gromdimon (3)
Top Labels
Issue Labels
enhancement (4) bug (2) dependencies (2)
Pull Request Labels
dependencies (135) python (18) autorelease: tagged (6) autorelease: pending (2)

Dependencies

.github/workflows/automerge.yml actions
.github/workflows/conventional-prs.yml actions
  • amannn/action-semantic-pull-request v3.4.0 composite
.github/workflows/docker-build.yml actions
  • actions/checkout v4 composite
  • docker/build-push-action v4 composite
  • docker/login-action v2 composite
  • docker/metadata-action v4 composite
.github/workflows/main.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v4 composite
  • codecov/codecov-action v3 composite
  • khan/pull-request-workflow-cancel 1.0.0 composite
.github/workflows/release-please.yml actions
  • GoogleCloudPlatform/release-please-action v2 composite
utils/docker/Dockerfile docker
  • base latest build
  • python 3.10-slim build
Pipfile pypi
  • black * develop
  • flake8 * develop
  • isort * develop
  • mypy * develop
  • pytest * develop
  • pytest-coverage * develop
  • cdot *
  • fastapi *
Pipfile.lock pypi
  • black ==23.9.1 develop
  • click ==8.1.7 develop
  • coverage ==7.3.1 develop
  • exceptiongroup ==1.1.3 develop
  • flake8 ==6.1.0 develop
  • iniconfig ==2.0.0 develop
  • isort ==5.12.0 develop
  • mccabe ==0.7.0 develop
  • mypy ==1.5.1 develop
  • mypy-extensions ==1.0.0 develop
  • packaging ==23.2 develop
  • pathspec ==0.11.2 develop
  • platformdirs ==3.10.0 develop
  • pluggy ==1.3.0 develop
  • pycodestyle ==2.11.0 develop
  • pyflakes ==3.1.0 develop
  • pytest ==7.4.2 develop
  • pytest-cov ==4.1.0 develop
  • pytest-cover ==3.0.0 develop
  • pytest-coverage ==0.0 develop
  • tomli ==2.0.1 develop
  • typing-extensions ==4.8.0 develop
  • annotated-types ==0.5.0
  • anyio ==3.7.1
  • attrs ==23.1.0
  • bioutils ==0.5.8.post1
  • cdot ==0.2.21
  • certifi ==2023.7.22
  • charset-normalizer ==3.3.0
  • exceptiongroup ==1.1.3
  • fastapi ==0.103.2
  • idna ==3.4
  • intervaltree ==3.1.0
  • lazy ==1.6
  • pydantic ==2.4.2
  • pydantic-core ==2.10.1
  • requests ==2.31.0
  • sniffio ==1.3.0
  • sortedcontainers ==2.4.0
  • starlette ==0.27.0
  • typing-extensions ==4.8.0
  • urllib3 ==1.26.16