Ragout | Chromosome-level scaffolding using multiple references | Genomics library

by fenderglass Python Version: 2.3 License: Non-SPDX

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

kandi X-RAY | Ragout Summary

Ragout is a Python library typically used in Artificial Intelligence, Genomics applications. Ragout has no bugs, it has no vulnerabilities, it has build file available and it has low support. However Ragout has a Non-SPDX License. You can download it from GitHub.

Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome-level scaffolding using multiple references. Given initial assembly fragments (contigs/scaffolds) and one or multiple related references (complete or draft), it produces a chromosome-scale assembly (as a set of scaffolds). The approach is based on the analysis of genome rearrangements (like inversions or chromosomal translocations) between the input genomes and reconstructing the most parsimonious structure of the target genome. Ragout now supports both small and large genomes (of mammalian scale and complexity). The assembly of highly polymorphic genomes is currently limited.

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Quality

Security

License

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Support

Ragout has a low active ecosystem.

It has 133 star(s) with 27 fork(s). There are 15 watchers for this library.

It had no major release in the last 12 months.

There are 9 open issues and 69 have been closed. On average issues are closed in 240 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of Ragout is 2.3

Quality

Ragout has 0 bugs and 0 code smells.

Security

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

Ragout code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

Ragout has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

Ragout releases are available to install and integrate.

Build file is available. You can build the component from source.

Ragout saves you 2384 person hours of effort in developing the same functionality from scratch.

It has 5199 lines of code, 392 functions and 58 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

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

Run Wagout
Clear the debug directory
Remove chimera adjacencies from a perm_container
Break a permutation
Resolve repeat blocks
Calculates the similarity between target_contexts
Get contexts from permutations
Compute the max weighting of a graph
Scale the tree
Get blocks from alignment
Run maf2synteny module
Filters out indels from the recipe
Count the number of breakpoints in the scaffolds
Count the number of adjoints in the graph
Load a module
Build from a perm_container
Builds adjacency graph
Install Sibelia
Refine scaffolds
Perform DFS traversal
Merge two scaffolds
Perform a single alignment
Returns a 2 - line breakpoint graph
Calculate hierarchical breaks for each branch
Runs the recipe
Assign scaffolds to scaffolds

Get all kandi verified functions for this library.

Ragout Key Features

No Key Features are available at this moment for Ragout.

Ragout Examples and Code Snippets

No Code Snippets are available at this moment for Ragout.

Community Discussions

Trending Discussions on Ragout

Android Room Write Custom Nested Objects

QUESTION

Android Room Write Custom Nested Objects

Asked 2020-Jul-31 at 13:07

Okay so I've successfully sent GET request to a server using Retrofit library, and parsed that data in my app. Now I want to store that data(custom model classes which I have created) in ROOM database, however I have a lot of model classes. So what's the best way to write that custom objects in database, how should I write type converters for this? Check my network response to understand how complex the data is:

...

ANSWER

Answered 2020-Jul-31 at 13:07

Although there's no best way of handling this, besides having to create converters models for each of these fields, it would be wise to limit the amount of data you're saving to only the relevant information that you're going to need and then to use custom converters to convert your data automatically.

As requested by OP in the comments, here's a basic example of how you can add a type converter for a list/array (making use of Gson):

extension methods:

Source https://stackoverflow.com/questions/63191828

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

Vulnerabilities

No vulnerabilities reported

Install Ragout

You can download it from GitHub.
You can use Ragout 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

Mikhail Kolmogorov (St. Petersburg University of the Russian Academy of Sciences, UCSD). Pavel Avdeev (St. Petersburg University of the Russian Academy of Sciences). Dmitriy Meleshko (St. Petersburg University of the Russian Academy of Sciences).

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