https://github.com/clinical-genomics/chanjo

Chanjo provides a better way to analyze coverage data in clinical sequencing.

Science Score: 13.0%

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
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.zenodo.json file
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DOI references
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Scientific vocabulary similarity
Low similarity (17.6%) to scientific vocabulary

Keywords

bioconda coverage genomics python sambamba sql

Keywords from Contributors

bioinformatics sequencing projection archival pypi reporting parallel generic control interactive

Last synced: 5 months ago · JSON representation

Repository

Chanjo provides a better way to analyze coverage data in clinical sequencing.

Basic Info

Host: GitHub
Owner: Clinical-Genomics
License: mit
Language: Python
Default Branch: main
Homepage: https://clinical-genomics.github.io/chanjo/
Size: 14.7 MB

Statistics

Stars: 51
Watchers: 9
Forks: 12
Open Issues: 31
Releases: 12

Topics

bioconda coverage genomics python sambamba sql

Created over 12 years ago · Last pushed about 1 year ago

Metadata Files

Readme Changelog Contributing License Authors

Chanjo

Chanjo is coverage analysis for clinical sequencing. It's implemented in Python with a command line interface that adheres to UNIX pipeline philosophy.

If you find chanjo useful in your project, please cite the article.

Installation

Chanjo is distributed through pip. Install the latest stable release by running:

bash pip install chanjo

... or locally for development:

bash git clone https://github.com/Clinical-Genomics/chanjo.git cd chanjo conda install --channel bioconda sambamba pip install -r requirements-dev.txt --editable .

Usage

Chanjo exposes a decomposable command line interface with a nifty config file implementation.

bash chanjo init --setup chanjo load /path/to/sambamba.output.bed chanjo calculate mean {"metrics": {"completeness_10": 90.92, "mean_coverage": 193.85}, "sample_id": "sample1"}

Docker

When running the dockerized version of Chanjo the setup process is slightly different. Chanjo depends on a configuration file config.yaml and either a sqlite database chanjo.coverage.sqlite3 or a MySQL database, which are created at initialization. For convenience, we provide a docker-compose file containing a mariadb (MySQL-based) service and the chanjo-command line that can be used to set up a demo instance of Chanjo. Since the database set up (chanjo init command) and sample data insertion are executed by two distinct instances of the same service (chanjo-cli), Docker volumes must be used to make sure that the database instance has data continuity during the two steps. The following examples demonstrate how to set up Chanjo using the docker-compose file using the default definition of exons (init demo files are present in folder chanjo/init/demo-files). The config file and the creted database will be stored on the host in a folder named data, which is mirrored by folder /home/worker/data in the chanjo container . Other exon definitions can be used by mounting them to the container.

Example with MySQL-based database (MariaDB)

```bash

Build a docker image

docker-compose build bash

Set up chanjo and populate demo database with exons definitions

docker-compose run --rm -v "${PWD}/data:/home/worker/data" -v "${PWD}/data/database:/home/worker/data/database" chanjo-cli bash -c "chanjo -d mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo4test init --auto /home/worker/data && chanjo --config /home/worker/data/chanjo.yaml link /home/worker/data/hgnc.grch37p13.exons.bed" ``This initial step will create adatafolder containing 2 files: - hgnc.grch37p13.exons.bed --> Exons definitions - chanjo.yaml --> Contains the database URI, so in the next step you can use this config file instead of-d mysql+pymysql://chanjoUser:chanjoPassword@mariadb/chanjo4test`

```bash

Load sample

docker-compose run --rm -v "${PWD}/data:/home/worker/data" -v "${PWD}/data/database:/home/worker/data/database" chanjo-cli bash -c "chanjo --config /home/worker/data/chanjo.yaml load /home/worker/app/chanjo/init/demo-files/sample1.coverage.bed" ```

Example with SQLite database

```bash

setup chanjo and save populate demo database with exon definitions

docker-compose run --rm -v "${PWD}/data:/home/worker/data" -v "${PWD}/data/database:/home/worker/data/database" chanjo-cli bash -c "chanjo init --auto /home/worker/data && chanjo --config /home/worker/data/chanjo.yaml link /home/worker/data/hgnc.grch37p13.exons.bed"

load sample

docker-compose run --rm -v "${PWD}/data/chanjo.coverage.sqlite3:/home/worker/app/chanjo.coverage.sqlite3" -v "${PWD}/data:/home/worker/data" chanjo-cli bash -c "chanjo --config /home/worker/data/chanjo.yaml load /home/worker/app/chanjo/init/demo-files/sample1.coverage.bed"

Documentation

Read the Docs is hosting the official documentation.

If you are looking to learn more about handling sequence coverage data in clinical sequencing, feel free to download and skim through my own Master's thesis and article references.

Features

What Chanjo does

Chanjo leverages Sambamba to annotate coverage and completeness for a general BED-file. The output can then easily to loaded into a SQL database that enables investigation of coverage across regions and samples. The database also works as an API to downstream tools like the Chanjo Coverage Report generator.

What Chanjo doesn't

Chanjo is not the right choice if you care about coverage for every base across the entire genome. Detailed histograms is something BEDTools already handles with confidence.

Contributors

Robin Andeer (robinandeer)
Luca Beltrame (lbeltrame)
John Kern (kern3020)
Måns Magnusson (moonso)
Patrik Grenfeldt (patrikgrenfeldt)

License

MIT. See the LICENSE file for more details.

Contributing

Anyone can help make this project better - read CONTRIBUTION to get started!

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

Issues event: 9
Watch event: 1
Delete event: 15
Issue comment event: 16
Push event: 21
Pull request review event: 5
Pull request review comment event: 9
Pull request event: 16
Create event: 5

Last Year

Issues event: 9
Watch event: 1
Delete event: 15
Issue comment event: 16
Push event: 21
Pull request review event: 5
Pull request review comment event: 9
Pull request event: 16
Create event: 5

Committers

Last synced: 9 months ago

All Time

Total Commits: 741
Total Committers: 18
Avg Commits per committer: 41.167
Development Distribution Score (DDS): 0.132

Past Year

Commits: 12
Committers: 4
Avg Commits per committer: 3.0
Development Distribution Score (DDS): 0.667

Top Committers

Name	Email	Commits
Robin Andeer	r**r@g**m	643
Chiara Rasi	r**a@g**m	21
moonso	m**s@g**m	19
John Kern	k**0@g**m	10
Patrik Grenfeldt	p**t@s**e	10
Robin Andeer	r**r@g**e	5
Chiara Rasi	r**a@g**m	5
Daniel Nilsson	d**n@g**m	5
adrosenbaum	4****m	5
Luca Beltrame	l**e@m**t	4
Måns Magnusson	m**n@s**e	3
Barry Stokman	2****n	2
Bitdeli Chef	c**f@b**m	2
Henrik Stranneheim	h**m@s**e	2
Robin Andeer	r**r@s**e	2
ChristianOertlin	c**n@g**m	1
Paulo Nuin	n**n@g**g	1
dependabot[bot]	4****]	1

Committer Domains (Top 20 + Academic)

scilifelab.se: 4 genedrift.org: 1 bitdeli.com: 1 marionegri.it: 1 gmacil.com: 1 gmail.se: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time

Total issues: 117
Total pull requests: 15
Average time to close issues: 3 months
Average time to close pull requests: 8 days
Total issue authors: 5
Total pull request authors: 4
Average comments per issue: 0.97
Average comments per pull request: 1.53
Merged pull requests: 14
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

robinandeer (70)
lbeltrame (9)
kern3020 (8)
dnil (3)
northwestwitch (3)
dgaston (1)
pekrau (1)

Pull Request Authors

dependabot[bot] (9)
northwestwitch (5)
kern3020 (4)
dnil (4)
lbeltrame (3)
moonso (2)
robinandeer (2)
ChrOertlin (1)
bitdeli-chef (1)

Top Labels

Issue Labels

enhancement (21) bug (20) question (13) wanted (12) needed (8) priority (6) on hold (4)

Pull Request Labels

dependencies (9)

Packages

Total packages: 1
Total downloads:
- pypi 2,575 last-month

Total dependent packages: 2
Total dependent repositories: 4
Total versions: 65
Total maintainers: 3

pypi.org: chanjo

Coverage analysis tool for clinical sequencing

Homepage: https://clinical-genomics.github.io/chanjo/
Documentation: https://chanjo.readthedocs.io/
License: MIT
Latest release: 4.7.2
published about 1 year ago

Versions: 65
Dependent Packages: 2
Dependent Repositories: 4
Downloads: 2,575 Last month

Rankings

Dependent packages count: 3.2%

Average: 6.6%

Dependent repos count: 7.5%

Downloads: 9.3%

Maintainers (3)

clingen moonso northwestwitch

Last synced: 6 months ago

Dependencies

Pipfile pypi

coveralls * develop
ipdb * develop
markdown-include * develop
mkdocs * develop
mock * develop
pylint * develop
pytest * develop
pytest-cov * develop
alchy *
click *
coloredlogs *
path *
ruamel.yaml *
toolz *

Pipfile.lock pypi

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ipython ==7.13.0 develop
ipython-genutils ==0.2.0 develop
isort ==4.3.21 develop
jedi ==0.17.0 develop
jinja2 ==2.11.2 develop
joblib ==0.14.1 develop
lazy-object-proxy ==1.4.3 develop
livereload ==2.6.1 develop
lunr ==0.5.6 develop
markdown ==3.2.1 develop
markdown-include ==0.5.1 develop
markupsafe ==1.1.1 develop
mccabe ==0.6.1 develop
mkdocs ==1.1 develop
mock ==4.0.2 develop
more-itertools ==8.2.0 develop
nltk ==3.5 develop
packaging ==20.3 develop
parso ==0.7.0 develop
pexpect ==4.8.0 develop
pickleshare ==0.7.5 develop
pluggy ==0.13.1 develop
prompt-toolkit ==3.0.5 develop
ptyprocess ==0.6.0 develop
py ==1.8.1 develop
pygments ==2.6.1 develop
pylint ==2.4.4 develop
pyparsing ==2.4.7 develop
pytest ==5.4.1 develop
pytest-cov ==2.8.1 develop
pyyaml ==5.3.1 develop
regex ==2020.4.4 develop
requests ==2.23.0 develop
six ==1.14.0 develop
tornado ==6.0.4 develop
tqdm ==4.45.0 develop
traitlets ==4.3.3 develop
typed-ast ==1.4.1 develop
urllib3 ==1.25.9 develop
wcwidth ==0.1.9 develop
wrapt ==1.11.2 develop
zipp ==3.1.0 develop
alchy ==2.2.2
click ==7.1.1
coloredlogs ==14.0
humanfriendly ==8.2
importlib-metadata ==1.6.0
path ==13.1.0
path.py ==12.4.0
pydash ==4.7.6
ruamel.yaml ==0.16.10
ruamel.yaml.clib ==0.2.0
sqlalchemy ==1.3.16
toolz ==0.10.0
zipp ==3.1.0

requirements-dev.txt pypi

coveralls * development
docutils * development
git-lint * development
html-linter * development
ipdb * development
markdown-include * development
mkdocs * development
mock * development
pycodestyle * development
pylint * development
pytest >=3.6 development
pytest-cov * development
yamllint * development

requirements.txt pypi

alchy *
click *
coloredlogs *
importlib_metadata *
path.py *
pymysql *
ruamel.yaml *
sqlalchemy ==1.3.
toolz *

.github/workflows/deploy_mkdocs.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/docker_build_n_publish.yml actions

actions/checkout v2 composite
elgohr/Publish-Docker-Github-Action master composite

.github/workflows/pypi_build_n_publish.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
pypa/gh-action-pypi-publish master composite

.github/workflows/pytest_n_coveralls.yml actions

actions/checkout v2 composite
actions/setup-python master composite

Dockerfile docker

frolvlad/alpine-miniconda3 latest build

docker-compose.yml docker

mariadb latest

https://github.com/clinical-genomics/chanjo

Science Score: 13.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Chanjo

Installation

Usage

Docker

Example with MySQL-based database (MariaDB)

Build a docker image

Set up chanjo and populate demo database with exons definitions

Load sample

Example with SQLite database

setup chanjo and save populate demo database with exon definitions

load sample

Documentation

Features

What Chanjo does

What Chanjo doesn't

Contributors

License

Contributing

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: chanjo

Rankings

Maintainers (3)

Dependencies