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

Clinical-Genomics, updated 🕥 2023-02-10 22:49:22

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:[email protected]/chanjo4_test 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:[email protected]/chanjo4_test`

```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!

Issues

Bump ipython from 7.13.0 to 8.10.0

opened on 2023-02-10 22:49:18 by dependabot[bot]

Bumps ipython from 7.13.0 to 8.10.0.

Release notes

Sourced from ipython's releases.

See https://pypi.org/project/ipython/

We do not use GitHub release anymore. Please see PyPI https://pypi.org/project/ipython/

Commits

15ea1ed release 8.10.0
560ad10 DOC: Update what's new for 8.10 (#13939)
7557ade DOC: Update what's new for 8.10
385d693 Merge pull request from GHSA-29gw-9793-fvw7
e548ee2 Swallow potential exceptions from showtraceback() (#13934)
0694b08 MAINT: mock slowest test. (#13885)
8655912 MAINT: mock slowest test.
a011765 Isolate the attack tests with setUp and tearDown methods
c7a9470 Add some regression tests for this change
fd34cf5 Swallow potential exceptions from showtraceback()
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Bump certifi from 2020.4.5.1 to 2022.12.7

opened on 2022-12-08 09:32:58 by dependabot[bot]

Bumps certifi from 2020.4.5.1 to 2022.12.7.

Commits

9e9e840 2022.12.07
b81bdb2 2022.09.24
939a28f 2022.09.14
aca828a 2022.06.15.2
de0eae1 Only use importlib.resources's new files() / Traversable API on Python ≥3.11 ...
b8eb5e9 2022.06.15.1
47fb7ab Fix deprecation warning on Python 3.11 (#199)
b0b48e0 fixes #198 -- update link in license
9d514b4 2022.06.15
4151e88 Add py.typed to MANIFEST.in to package in sdist (#196)
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Bump joblib from 0.14.1 to 1.2.0

opened on 2022-09-30 19:06:15 by dependabot[bot]

Bumps joblib from 0.14.1 to 1.2.0.

Changelog

Sourced from joblib's changelog.

Release 1.2.0

Fix a security issue where eval(pre_dispatch) could potentially run arbitrary code. Now only basic numerics are supported. joblib/joblib#1327

Make sure that joblib works even when multiprocessing is not available, for instance with Pyodide joblib/joblib#1256

Avoid unnecessary warnings when workers and main process delete the temporary memmap folder contents concurrently. joblib/joblib#1263

Fix memory alignment bug for pickles containing numpy arrays. This is especially important when loading the pickle with mmap_mode != None as the resulting numpy.memmap object would not be able to correct the misalignment without performing a memory copy. This bug would cause invalid computation and segmentation faults with native code that would directly access the underlying data buffer of a numpy array, for instance C/C++/Cython code compiled with older GCC versions or some old OpenBLAS written in platform specific assembly. joblib/joblib#1254

Vendor cloudpickle 2.2.0 which adds support for PyPy 3.8+.

Vendor loky 3.3.0 which fixes several bugs including:

robustly forcibly terminating worker processes in case of a crash (joblib/joblib#1269);

avoiding leaking worker processes in case of nested loky parallel calls;

reliability spawn the correct number of reusable workers.

Release 1.1.0

Fix byte order inconsistency issue during deserialization using joblib.load in cross-endian environment: the numpy arrays are now always loaded to use the system byte order, independently of the byte order of the system that serialized the pickle. joblib/joblib#1181

Fix joblib.Memory bug with the ignore parameter when the cached function is a decorated function.

... (truncated)

Commits

5991350 Release 1.2.0
3fa2188 MAINT cleanup numpy warnings related to np.matrix in tests (#1340)
cea26ff CI test the future loky-3.3.0 branch (#1338)
8aca6f4 MAINT: remove pytest.warns(None) warnings in pytest 7 (#1264)
067ed4f XFAIL test_child_raises_parent_exits_cleanly with multiprocessing (#1339)
ac4ebd5 MAINT add back pytest warnings plugin (#1337)
a23427d Test child raises parent exits cleanly more reliable on macos (#1335)
ac09691 [MAINT] various test updates (#1334)
4a314b1 Vendor loky 3.2.0 (#1333)
bdf47e9 Make test_parallel_with_interactively_defined_functions_default_backend timeo...
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Bump mkdocs from 1.1 to 1.2.3

opened on 2022-05-16 16:44:42 by dependabot[bot]

Bumps mkdocs from 1.1 to 1.2.3.

Release notes

Sourced from mkdocs's releases.

1.2.3

MkDocs 1.2.3 is a bugfix release for MkDocs 1.2.

Aside: MkDocs has a new chat room on Gitter/Matrix. More details.

Improvements:

Built-in themes now also support these languages:

Simplified Chinese (#2497)

Japanese (#2525)

Brazilian Portuguese (#2535)

Spanish (#2545, previously #2396)

Third-party plugins will take precedence over built-in plugins with the same name (#2591)

Bugfix: Fix ability to load translations for some languages: core support (#2565) and search plugin support with fallbacks (#2602)

Bugfix (regression in 1.2): Prevent directory traversal in the dev server (#2604)

Bugfix (regression in 1.2): Prevent webserver warnings from being treated as a build failure in strict mode (#2607)

Bugfix: Correctly print colorful messages in the terminal on Windows (#2606)

Bugfix: Python version 3.10 was displayed incorrectly in --version (#2618)

Other small improvements; see commit log.

1.2.2

MkDocs 1.2.2 is a bugfix release for MkDocs 1.2 -- make sure you've seen the "major" release notes as well.

Bugfix (regression in 1.2): Fix serving files/paths with Unicode characters (#2464)

Bugfix (regression in 1.2): Revert livereload file watching to use polling observer (#2477)

This had to be done to reasonably support usages that span virtual filesystems such as non-native Docker and network mounts.

This goes back to the polling approach, very similar to that was always used prior, meaning most of the same downsides with latency and CPU usage.

Revert from 1.2: Remove the requirement of a site_url config and the restriction on use_directory_urls (#2490)

Bugfix (regression in 1.2): Don't require trailing slash in the URL when serving a directory index in mkdocs serve server (#2507)

Instead of showing a 404 error, detect if it's a directory and redirect to a path with a trailing slash added, like before.

Bugfix: Fix gh_deploy with config-file in the current directory (#2481)

Bugfix: Fix reversed breadcrumbs in "readthedocs" theme (#2179)

Allow "mkdocs.yaml" as the file name when '--config' is not passed (#2478)

... (truncated)

Commits

d167eab Release 1.2.3 (#2614)
5629b09 Re-format translation files to pass a lint check (#2621)
2c4679b Re-format translation files to pass a lint check (#2620)
9262cc5 Fix the code to abbreviate Python's version (#2618)
8345850 Add hint about -f/--config-file in configuration documentation (#2616)
815af48 Added translation for Brazilian Portuguese (#2535)
6563439 Update contact instructions: announce chat, preference for issues (#2610)
6b72eef We can again announce support of zh_CN locale (#2609)
b18ae29 Drop assert_mock_called_once compat method from tests (#2611)
7a27572 Isolate strict warning counter to just the ongoing build (#2607)
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Bump nltk from 3.5 to 3.6.6

opened on 2022-05-16 16:42:24 by dependabot[bot]

Bumps nltk from 3.5 to 3.6.6.

Changelog

Sourced from nltk's changelog.

Version 3.7 2022-02-09

Improve and update the NLTK team page on nltk.org (#2855, #2941)

Drop support for Python 3.6, support Python 3.10 (#2920)

Version 3.6.7 2021-12-28

Resolve IndexError in sent_tokenize and word_tokenize (#2922)

Version 3.6.6 2021-12-21

Refactor gensim.doctest to work for gensim 4.0.0 and up (#2914)

Add Precision, Recall, F-measure, Confusion Matrix to Taggers (#2862)

Added warnings if .zip files exist without any corresponding .csv files. (#2908)

Fix FileNotFoundError when the download_dir is a non-existing nested folder (#2910)

Rename omw to omw-1.4 (#2907)

Resolve ReDoS opportunity by fixing incorrectly specified regex (#2906)

Support OMW 1.4 (#2899)

Deprecate Tree get and set node methods (#2900)

Fix broken inaugural test case (#2903)

Use Multilingual Wordnet Data from OMW with newer Wordnet versions (#2889)

Keep NLTKs "tokenize" module working with pathlib (#2896)

Make prettyprinter to be more readable (#2893)

Update links to the nltk book (#2895)

Add CITATION.cff to nltk (#2880)

Resolve serious ReDoS in PunktSentenceTokenizer (#2869)

Delete old CI config files (#2881)

Improve Tokenize documentation + add TokenizerI as superclass for TweetTokenizer (#2878)

Fix expected value for BLEU score doctest after changes from #2572

Add multi Bleu functionality and tests (#2793)

Deprecate 'return_str' parameter in NLTKWordTokenizer and TreebankWordTokenizer (#2883)

Allow empty string in CFG's + more (#2888)

Partition tree.py module into tree package + pickle fix (#2863)

Fix several TreebankWordTokenizer and NLTKWordTokenizer bugs (#2877)

Rewind Wordnet data file after each lookup (#2868)

Correct init call for SyntaxCorpusReader subclasses (#2872)

Documentation fixes (#2873)

Fix levenstein distance for duplicated letters (#2849)

Support alternative Wordnet versions (#2860)

Remove hundreds of formatting warnings for nltk.org (#2859)

Modernize nltk.org/howto pages (#2856)

Fix Bleu Score smoothing function from taking log(0) (#2839)

Update third party tools to newer versions and removing MaltParser fixed version (#2832)

Fix TypeError: _pretty() takes 1 positional argument but 2 were given in sem/drt.py (#2854)

Replace http with https in most URLs (#2852)

Thanks to the following contributors to 3.6.6 Adam Hawley, BatMrE, Danny Sepler, Eric Kafe, Gavish Poddar, Panagiotis Simakis, RnDevelover, Robby Horvath, Tom Aarsen, Yuta Nakamura, Mohaned Mashaly

... (truncated)

Commits

4862b09 updates for 3.6.6
6b60213 Refactor gensim.doctest to work for gensim 4.0.0 and up (#2914)
59aa3fb Fix decode error for bllip parser (#2897)
a28d256 Add Precision, Recall, F-measure, Confusion Matrix to Taggers (#2862)
72d9885 Added warnings if .zip files exist without any corresponding .csv files. (#2908)
dea7b44 Fix FileNotFoundError when the download_dir is a non-existing nested fold...
abbe86b Undo #2909 due to unexpected test failure
c075dab Allow commits with /nocache to not use the cache (#2909)
d6d513d Renamed omw to omw-1.4 (#2907)
2a50a3e Resolve ReDoS opportunity by fixing incorrectly specified regex (#2906)
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Fix query to avoid "GROUP BY clause; this is incompatible with sql_mode=only_full_group_by" error

opened on 2021-10-13 09:23:36 by northwestwitch

pymysql.err.OperationalError: (1055, "Expression #1 of SELECT list is not in GROUP BY clause and contains nonaggregated column 'chanjo4.transcript_stat.id' which is not functionally dependent on columns in GROUP BY clause; this is incompatible with sql_mode=only_full_group_by")

Releases

Chanjo 3.0.0 2015-10-26 08:13:05

A brand new release of Chanjo is upon us :tada:

This version integrates with Sambamba and drops Pysam/Samtools as a dependency. It also expands on the possibilities to directly calculate coverage metrics from the command line! Please refer to the updated documentation and the CHANGELOG for more on what's new - enjoy!

And a big thanks to @moonso who is joining as a new core contributor for this release :smile:

Get started by:

bash $ pip install --upgrade chanjo

Beta of the next major release of Chanjo 2015-09-03 13:55:27

We have really done a lot of work to clean up the interface You can now directly query the database for interesting coverage metrics We rely on Sambamba to generate coverage stats from BAM files

Public release (DOI) 2014-06-02 06:38:20

Chanjo can now be referenced in scientific journals using DOI.

New sample table 2013-10-22 09:12:23

Chanjo will now automatically keep track of which cutoff you used for completeness, creation dates, and source BAM file for each sample.

Also the docs have been updated with info on SQL structure

Multi sample support 2013-09-20 15:02:51

Chanjo is now able to handle multiple samples and store them in the same SQLite database. This is great for comparing different samples and keeping all coverage annotations in one place.

A lot of (breaking) changes has had to be made to get to this point. Do check out the updated "chanjo-autopilot" help text if you plan on using the CLI.

I've now also limited Chanjo in scope: it will be focused on reading coverage data and annotating elements. Everything else downstream will be handled by a separate, although, connected package. Announcement later :)

Lastly Chanjo now extends the SQL schema structure found in my own new Elemental DB project.

Base level resolution 2013-09-05 20:51:59

Read depth levels are now persisted in the SQLite database as a compressed BLOB. This is useful in the off chance that full base-level resolution is needed.

NOTICE: I've now decided the focus for Chanjo which will be threefold: 1. Setting up a datastore of elements, 2. Getting coverage data as a list of read depths, 3. Annotating elements with relevant coverage metrics.

Stay tuned to find out more about project integrating with Chanjo downstream!

Clinical Genomics

GitHub Repository Homepage

bioconda coverage sambamba python sql genomics