VCF-Simplify | A python parser to simplify and build the VCF | Genomics library
kandi X-RAY | VCF-Simplify Summary
kandi X-RAY | VCF-Simplify Summary
VCF-Simplify is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. VCF-Simplify has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.
A python parser to simplify and build the VCF (Variant Call Format).
A python parser to simplify and build the VCF (Variant Call Format).
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Quality
Security
License
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VCF-Simplify has a low active ecosystem.
It has 32 star(s) with 13 fork(s). There are 3 watchers for this library.
It had no major release in the last 12 months.
There are 2 open issues and 5 have been closed. On average issues are closed in 32 days. There are 1 open pull requests and 0 closed requests.
It has a neutral sentiment in the developer community.
The latest version of VCF-Simplify is v3.0.1
Quality
VCF-Simplify has 0 bugs and 0 code smells.
Security
VCF-Simplify has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
VCF-Simplify code analysis shows 0 unresolved vulnerabilities.
There are 0 security hotspots that need review.
License
VCF-Simplify is licensed under the MIT License. This license is Permissive.
Permissive licenses have the least restrictions, and you can use them in most projects.
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VCF-Simplify releases are available to install and integrate.
Build file is available. You can build the component from source.
Installation instructions, examples and code snippets are available.
VCF-Simplify saves you 653 person hours of effort in developing the same functionality from scratch.
It has 1516 lines of code, 75 functions and 23 files.
It has high code complexity. Code complexity directly impacts maintainability of the code.
Top functions reviewed by kandi - BETA
kandi has reviewed VCF-Simplify and discovered the below as its top functions. This is intended to give you an instant insight into VCF-Simplify implemented functionality, and help decide if they suit your requirements.
- Main function for simplification
- Convert a Table to a VCF file
- Convert a haplotype file into a VCF file
- Convert haplotypes to VCF format
- Argument parser for build VCF
- Parse command line options
- Parse a haplotype_to_vcf file
- Add command line options
- Parse VCF to haplotype output
- Decorator to measure memory memory
- Write the VCF records to the output file
- Write metadata to a table
- Group vcf records into a single dict
- Write vcf records as JSON
Get all kandi verified functions for this library.
VCF-Simplify Key Features
No Key Features are available at this moment for VCF-Simplify.
VCF-Simplify Examples and Code Snippets
No Code Snippets are available at this moment for VCF-Simplify.
Community Discussions
Trending Discussions on VCF-Simplify
QUESTION
Import file mismatch errors occurs when running complete test in pytest, but passed test when run separately
Asked 2019-Dec-22 at 18:11
When running the complete test with command python -m pytest tests, it fails with import file mismatch error.
ANSWER
Answered 2019-Dec-22 at 14:44Well this has been an issue specifically related to pytest so you shouldn't worry much about because it's only related to cached files.
step 1 remove all __pycache__ folders from your test directory.
step 2 add the following snippet in your bashrc/zshrc file depending on which you use to stop generating those caches.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install VCF-Simplify
Cythonize (Optional but helpful for faster performance).
Clone this repo
Cythonize (Optional but helpful for faster performance) Create and activate a virtual environment # create virtual environment named "myenv" python3 -m venv myenv # rename environment as required # activate the environment source myenv/bin/activate # for linux myenv\Scripts\activate # for windows Install Cython library (myenv)$ pip install Cython Cythonize (so that app runs faster) # cythoize using the 'setup.py' file in "VCF Simplify" (myenv)$ python3 setup.py build_ext --inplace This makes .so files in your build directory and it will be called when importing modules rather than actual modules.
Call VCFSimplify
ViewVCF, SimplifyVCF, BuildVCF.
Each function can be further expanded as shown in the "Usage" below.
Clone this repo
Cythonize (Optional but helpful for faster performance) Create and activate a virtual environment # create virtual environment named "myenv" python3 -m venv myenv # rename environment as required # activate the environment source myenv/bin/activate # for linux myenv\Scripts\activate # for windows Install Cython library (myenv)$ pip install Cython Cythonize (so that app runs faster) # cythoize using the 'setup.py' file in "VCF Simplify" (myenv)$ python3 setup.py build_ext --inplace This makes .so files in your build directory and it will be called when importing modules rather than actual modules.
Call VCFSimplify
ViewVCF, SimplifyVCF, BuildVCF.
Each function can be further expanded as shown in the "Usage" below.
Support
For any new features, suggestions and bugs create an issue on GitHub.
If you have any questions check and ask questions on community page Stack Overflow .
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