tskit | Population-scale genomics | Genomics library

by tskit-dev Python Version: 0.5.7 License: MIT

X-Ray Key Features Code Snippets(1)Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | tskit Summary

tskit is a Python library typically used in Artificial Intelligence, Genomics applications. tskit has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However tskit build file is not available. You can install using 'pip install tskit' or download it from GitHub, PyPI.

Succinct tree sequences are a highly efficient way of storing a set of related DNA sequences by encoding their ancestral history as a set of correlated trees along the genome. The tree sequence format is output by a number of software libraries and programs (such as msprime, SLiM, fwdpp, and tsinfer) that either simulate or infer the evolutionary history of genetic sequences. The evolutionary history of genetic sequences is often technically referred to as an Ancestral Recombination Graph (ARG); succinct tree sequences are fully compatible with this formulation, and tskit is a therefore a powerful platform for processing ARGs. The tskit library provides the underlying functionality used to load, examine, and manipulate tree sequences, including efficient methods for calculating genetic statistics. It often forms part of an installation of other software packages such as those listed above. Please see the documentation for further details, which includes installation instructions. Also see the road map for planned improvements and additions to the library. To get started with tskit, tutorials and other content are at For help and support from the community you can use discussions here on github, or raise an issue for a specific bug or feature request. We warmly welcome contributions from the community. Raise an issue if you have an idea you'd like to work on, or submit a PR for comments and help. The base tskit library provides both a Python and C API. A Rust API is provided in the tskit-rust repository.

Support

Quality

Security

License

Reuse

Support

tskit has a low active ecosystem.

It has 116 star(s) with 61 fork(s). There are 10 watchers for this library.

There were 1 major release(s) in the last 12 months.

There are 236 open issues and 831 have been closed. On average issues are closed in 147 days. There are 26 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of tskit is 0.5.7

Quality

tskit has no bugs reported.

Security

tskit has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

tskit 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

tskit releases are available to install and integrate.

Deployable package is available in PyPI.

tskit has no build file. You will be need to create the build yourself to build the component from source.

Top functions reviewed by kandi - BETA

kandi has reviewed tskit and discovered the below as its top functions. This is intended to give you an instant insight into tskit implemented functionality, and help decide if they suit your requirements.

Draws the tree
Return a Variant instance
Write the VCF file
Check that the genomic range is valid
Load text file
Parse edge table
Sort the table
Dump a text table to a text table
Return the node metadata
Return tree sequence as HTML
Dump a legacy hdf5 file
Writes a DNA sequence sequence
Parse a FASTA file
Return a subset of nodes
Load a legacy hdf5 file
Writes trees in tree format
Return argument parser
Simplify a structure
Split polytomies into polytomies
Assign the y coordinates of the tree
Draw a tree
Dump a legacy HDF5 file
Clip a tree sequence
Draws the x axis of the plot
Render a variant
Load a legacy hdf5 table

Get all kandi verified functions for this library.

tskit Key Features

No Key Features are available at this moment for tskit.

tskit Examples and Code Snippets

Passing an array to a function in reticulated Python

Python

Lines of Code : 26

License : Strong Copyleft (CC BY-SA 4.0)

Copy

demography <- msprime$Demography$isolated_model(draws[1,1], growth_rate = draws[1,2])

demography <- msprime$Demography$isolated_model(list(draws[1,1]), growth_rate = list(draws[1,2]))

Community Discussions

Trending Discussions on tskit

ld: library not found for

QUESTION

ld: library not found for

Asked 2020-May-07 at 13:30

I'm hitting a linker error (compile time, not run time):

...

ANSWER

Answered 2020-May-07 at 13:30

Your linkage command shows that your linker is the OS X linker. Refer to it's manual with respect to the -l option:

-lx

This option tells the linker to search for libx.dylib or libx.a in the library search path. If string x is of the form y.o, then that file is searched for in the same places, but without prepending lib or appending .a or .dylib to the filename.

This will show you why all of:

Source https://stackoverflow.com/questions/61649602

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install tskit

You can install using 'pip install tskit' or download it from GitHub, PyPI.
You can use tskit 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: