fastStructure | variational framework for inferring population structure | Genomics library
kandi X-RAY | fastStructure Summary
kandi X-RAY | fastStructure Summary
fastStructure is a Python library typically used in Artificial Intelligence, Genomics applications. fastStructure 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.
fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. Here, we summarize how to setup this software package, compile the C and Cython scripts and run the algorithm on a test simulated genotype dataset.
fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. Here, we summarize how to setup this software package, compile the C and Cython scripts and run the algorithm on a test simulated genotype dataset.
Support
Quality
Security
License
Reuse
Support
fastStructure has a low active ecosystem.
It has 117 star(s) with 50 fork(s). There are 11 watchers for this library.
It had no major release in the last 12 months.
There are 47 open issues and 15 have been closed. On average issues are closed in 135 days. There are 6 open pull requests and 0 closed requests.
It has a neutral sentiment in the developer community.
The latest version of fastStructure is v1.0
Quality
fastStructure has 0 bugs and 0 code smells.
Security
fastStructure has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
fastStructure code analysis shows 0 unresolved vulnerabilities.
There are 0 security hotspots that need review.
License
fastStructure is licensed under the MIT License. This license is Permissive.
Permissive licenses have the least restrictions, and you can use them in most projects.
Reuse
fastStructure releases are available to install and integrate.
Build file is available. You can build the component from source.
Installation instructions are not available. Examples and code snippets are available.
It has 345 lines of code, 12 functions and 6 files.
It has low code complexity. Code complexity directly impacts maintainability of the code.
Top functions reviewed by kandi - BETA
kandi has reviewed fastStructure and discovered the below as its top functions. This is intended to give you an instant insight into fastStructure implemented functionality, and help decide if they suit your requirements.
- Plot an admixture matrix .
- Calculate proportions of admixture proportions .
- Check options for convergence .
- Parse a list of VCF files .
- Parse log files .
- Write the output of the model .
- Parse options .
- Print usage information .
Get all kandi verified functions for this library.
fastStructure Key Features
No Key Features are available at this moment for fastStructure.
fastStructure Examples and Code Snippets
No Code Snippets are available at this moment for fastStructure.
Community Discussions
Trending Discussions on fastStructure
QUESTION
Error while running fastStructure: ImportError: No module named allelefreq
Asked 2018-Dec-27 at 06:38
I'm trying to run faststructure software. Aftering installing numpy, scipy, cython, gsl1.16, when I try to run "python structure.py",it gives the following error:
...ANSWER
Answered 2018-Dec-27 at 06:38I remember some new version of cython have some issues(Forget the detail), but downgrade cython version maybe a solution:
Like follows:
QUESTION
how to run STRUCTURE command n times for each k value?
Asked 2017-Jul-25 at 22:17
I am running some STRUCTURE analysis and set k = {1..10} by using this command (only 1 run for each K):
...ANSWER
Answered 2017-Jul-25 at 16:28You can use another seq call:
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install fastStructure
You can download it from GitHub.
You can use fastStructure like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
You can use fastStructure like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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 .
Find more information at:
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page
